Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xbk Working: het.cluster.ucsf.bkslab.org:/scratch/xiaobo/3016/xbk-8058097.37 Result: /scratch/xiaobo/3016/xbk-8058097.37 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbk 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/xbk mkdir: created directory `/scratch/xiaobo/3016' mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37' /scratch/xiaobo/3016/xbk-8058097.37 /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/3016/xbk-8058097.37/working' mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/protonate' Storing results in /scratch/xiaobo/3016/xbk-8058097.37/finished Working in /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 /scratch/xiaobo/3016/xbk-8058097.37/working/protonate /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Using inputs as protomers/tautomers. No processing done 491 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/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Bulk generating 3D conformations all protomers in /scratch/xiaobo/3016/xbk-8058097.37/working/3D mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/3016/xbk-8058097.37/working/protonate/xbk-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 ZINC001285359293 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building' mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359293 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/1 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285359293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285359293 none C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 17, 12, 17, 7, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/2 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285359293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285359293 none C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 17, 12, 17, 7, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359293 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/finished' Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 Building ZINC001285359293 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359293 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 1) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285359293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285359293 none C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 17, 12, 17, 7, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 2) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285359293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285359293 none C[C@H]1CCN(CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 17, 12, 17, 7, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359293 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359293 Building ZINC001285359312 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359312 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/3 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285359312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285359312 none CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 46, 50, 30, 44, 13, 30, 10, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 13, 13, 10, 10, 4, 4, 4, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/4 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285359312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285359312 none CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 25, 40, 10, 25, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 10, 10, 8, 8, 3, 3, 3, 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359312 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 Building ZINC001285359312 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359312 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 3) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285359312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285359312 none CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 46, 50, 30, 44, 13, 30, 10, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 13, 13, 10, 10, 4, 4, 4, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 4) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285359312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285359312 none CC(=O)N1CCC[C@H]1C(=O)N(C)CCN(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 25, 40, 10, 25, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 10, 10, 8, 8, 3, 3, 3, 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359312 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359312 Building ZINC001285359385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/5 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O) `ZINC001285359385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359385 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 38, 41, 45, 45, 45, 45, 45, 45, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/6 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O) `ZINC001285359385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359385 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 35, 38, 44, 44, 44, 44, 44, 44, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 Building ZINC001285359385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 5) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O) `ZINC001285359385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359385 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 38, 41, 45, 45, 45, 45, 45, 45, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 6) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O) `ZINC001285359385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359385 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 35, 38, 44, 44, 44, 44, 44, 44, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359385 Building ZINC001285359386 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359386 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/7 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O) `ZINC001285359386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359386 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 31, 36, 46, 46, 46, 46, 46, 46, 50, 50, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/8 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O) `ZINC001285359386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359386 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 35, 39, 46, 46, 46, 46, 46, 46, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359386 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 Building ZINC001285359386 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359386 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 7) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O) `ZINC001285359386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359386 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 31, 36, 46, 46, 46, 46, 46, 46, 50, 50, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 8) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O) `ZINC001285359386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359386 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 35, 39, 46, 46, 46, 46, 46, 46, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359386 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359386 Building ZINC001285359387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/9 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O) `ZINC001285359387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359387 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 36, 39, 42, 44, 44, 44, 44, 44, 50, 50, 19, 19, 19, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/10 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O) `ZINC001285359387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359387 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 38, 41, 44, 46, 46, 46, 46, 46, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 Building ZINC001285359387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 9) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O) `ZINC001285359387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359387 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 36, 39, 42, 44, 44, 44, 44, 44, 50, 50, 19, 19, 19, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 10) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O) `ZINC001285359387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359387 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 38, 41, 44, 46, 46, 46, 46, 46, 50, 50, 18, 18, 18, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359387 Building ZINC001285359388 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359388 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/11 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O) `ZINC001285359388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359388 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 35, 39, 46, 46, 46, 46, 46, 46, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/12 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O) `ZINC001285359388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359388 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 31, 36, 46, 46, 46, 46, 46, 46, 50, 50, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359388 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 Building ZINC001285359388 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359388 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 11) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O) `ZINC001285359388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359388 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 35, 39, 46, 46, 46, 46, 46, 46, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 12) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O) `ZINC001285359388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359388 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 14, 31, 36, 46, 46, 46, 46, 46, 46, 50, 50, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359388 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359388 Building ZINC001285359776 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359776 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/13 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285359776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359776 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/14 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285359776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359776 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359776 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 Building ZINC001285359776 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359776 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 13) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285359776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359776 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 14) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285359776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359776 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359776 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359776 Building ZINC001285359777 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359777 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/15 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285359777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359777 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 39, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/16 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285359777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359777 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359777 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 Building ZINC001285359777 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359777 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 15) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285359777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359777 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 39, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 16) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285359777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359777 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359777 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359777 Building ZINC001285359789 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359789 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/17 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1) `ZINC001285359789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359789 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [18, 8, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 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, 52]) total number of confs: 133 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/18 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1) `ZINC001285359789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359789 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 31, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 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, 52]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359789 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 Building ZINC001285359789 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359789 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 17) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1) `ZINC001285359789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359789 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [18, 8, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 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, 52]) total number of confs: 133 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 18) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1) `ZINC001285359789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359789 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 31, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 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, 52]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359789 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359789 Building ZINC001285359790 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359790 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/19 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1) `ZINC001285359790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359790 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 32, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 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, 52]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/20 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1) `ZINC001285359790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359790 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 8, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 32, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 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, 52]) total number of confs: 137 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359790 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 Building ZINC001285359790 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359790 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 19) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1) `ZINC001285359790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359790 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 32, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 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, 52]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 20) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1) `ZINC001285359790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359790 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCn2ccnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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: [19, 8, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 32, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 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, 52]) total number of confs: 137 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359790 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359790 Building ZINC001285359799 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359799 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/21 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285359799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359799 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 6, 39, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 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, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/22 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285359799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359799 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 6, 39, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 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, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359799 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 Building ZINC001285359799 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359799 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 21) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285359799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359799 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 6, 39, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 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, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 22) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285359799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359799 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 19, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 6, 39, 8, 9, 10, 11, 12, 13, 46, 44, 40, 41, 47, 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, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359799 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359799 Building ZINC001285359919 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359919 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/23 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001285359919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359919 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 19, 23, 23, 34, 34, 50, 50, 14, 14, 14, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 23, 23, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/24 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001285359919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359919 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 23, 23, 32, 32, 50, 50, 12, 12, 12, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 23, 23, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359919 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 Building ZINC001285359919 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359919 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 23) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001285359919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359919 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 19, 23, 23, 34, 34, 50, 50, 14, 14, 14, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 23, 23, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 24) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001285359919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359919 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 23, 23, 32, 32, 50, 50, 12, 12, 12, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 23, 23, 23, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359919 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359919 Building ZINC001285359942 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359942 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/25 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1) `ZINC001285359942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359942 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 7, 7, 14, 32, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/26 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1) `ZINC001285359942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359942 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 13, 32, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359942 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 Building ZINC001285359942 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285359942 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 25) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1) `ZINC001285359942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285359942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359942 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 7, 7, 14, 32, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 26) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1) `ZINC001285359942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285359942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285359942 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 13, 32, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285359942 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285359942 Building ZINC001285360727 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360727 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/27 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1) `ZINC001285360727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360727 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 38, 50, 50, 50, 50, 50, 50, 23, 23, 23, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/28 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1) `ZINC001285360727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360727 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360727 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 Building ZINC001285360727 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360727 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 27) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1) `ZINC001285360727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360727 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 38, 50, 50, 50, 50, 50, 50, 23, 23, 23, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 28) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1) `ZINC001285360727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360727 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360727 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360727 Building ZINC001285360728 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360728 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/29 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1) `ZINC001285360728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360728 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 36, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/30 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1) `ZINC001285360728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360728 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 37, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360728 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 Building ZINC001285360728 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360728 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 29) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1) `ZINC001285360728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360728 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 36, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 30) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1) `ZINC001285360728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360728 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 37, 50, 50, 50, 50, 50, 50, 22, 22, 22, 9, 9, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360728 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360728 Building ZINC001285360981 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360981 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/31 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1) `ZINC001285360981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360981 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 29, 29, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/32 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1) `ZINC001285360981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360981 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 28, 28, 48, 48, 48, 48, 50, 50, 48, 48, 15, 15, 15, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360981 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 Building ZINC001285360981 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285360981 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 31) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1) `ZINC001285360981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285360981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360981 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 29, 29, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 32) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1) `ZINC001285360981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285360981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285360981 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.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, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 28, 28, 48, 48, 48, 48, 50, 50, 48, 48, 15, 15, 15, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285360981 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285360981 Building ZINC001285361017 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361017 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/33 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1) `ZINC001285361017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361017 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/34 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1) `ZINC001285361017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361017 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361017 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 Building ZINC001285361017 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361017 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 33) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1) `ZINC001285361017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361017 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 34) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1) `ZINC001285361017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361017 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361017 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361017 Building ZINC001285361031 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361031 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/35 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285361031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361031 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 36, 36, 36, 50, 50, 36, 36, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 36, 36] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/36 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285361031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361031 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 35, 35, 35, 35, 35, 35, 50, 50, 35, 35, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 35, 35] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361031 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 Building ZINC001285361031 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361031 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 35) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285361031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361031 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 36, 36, 36, 50, 50, 36, 36, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 36, 36] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 36) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285361031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361031 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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: [20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 35, 35, 35, 35, 35, 35, 50, 50, 35, 35, 20, 20, 20, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 35, 35] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361031 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361031 Building ZINC001285361032 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361032 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/37 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285361032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361032 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/38 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285361032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361032 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361032 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 Building ZINC001285361032 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361032 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 37) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285361032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361032 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 38) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285361032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361032 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 16, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361032 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361032 Building ZINC001285361037 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361037 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/39 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O) `ZINC001285361037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361037 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 13, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 25, 40, 47, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/40 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O) `ZINC001285361037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361037 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 16, 14, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 47, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 16, 16, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361037 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 Building ZINC001285361037 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361037 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 39) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O) `ZINC001285361037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361037 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 13, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 25, 40, 47, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 40) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O) `ZINC001285361037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361037 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 16, 14, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 47, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 16, 16, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361037 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361037 Building ZINC001285361038 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361038 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/41 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O) `ZINC001285361038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361038 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 13, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 25, 42, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 15, 15, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/42 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O) `ZINC001285361038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361038 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 12, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 24, 40, 47, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 13, 13, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361038 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 Building ZINC001285361038 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361038 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 41) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O) `ZINC001285361038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361038 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 13, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 25, 42, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 15, 15, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 42) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O) `ZINC001285361038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361038 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 12, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 24, 40, 47, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 13, 13, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361038 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361038 Building ZINC001285361332 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361332 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/43 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285361332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285361332 none Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 12, 8, 12, 6, 8, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 8, 8, 8, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/44 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285361332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285361332 none Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 12, 9, 12, 6, 9, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 9, 9, 9, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361332 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 Building ZINC001285361332 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361332 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 43) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285361332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285361332 none Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 12, 8, 12, 6, 8, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 8, 8, 8, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 44) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285361332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285361332 none Cc1nn(C)cc1CC(=O)N(C)CCN(C)C(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 12, 9, 12, 6, 9, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 9, 9, 9, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361332 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361332 Building ZINC001285361461 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361461 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/45 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1) `ZINC001285361461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285361461 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 25, 44, 44, 50, 50, 50, 50, 50, 50, 25, 25, 25, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/46 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1) `ZINC001285361461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285361461 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 26, 44, 44, 50, 50, 50, 50, 50, 50, 26, 26, 26, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361461 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 Building ZINC001285361461 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361461 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 45) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1) `ZINC001285361461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285361461 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 25, 44, 44, 50, 50, 50, 50, 50, 50, 25, 25, 25, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 46) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1) `ZINC001285361461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285361461 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 26, 44, 44, 50, 50, 50, 50, 50, 50, 26, 26, 26, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361461 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361461 Building ZINC001285361751 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361751 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/47 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285361751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285361751 none CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 42, 21, 42, 8, 21, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/48 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285361751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285361751 none CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 41, 21, 41, 7, 21, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 21, 21, 21, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361751 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 Building ZINC001285361751 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361751 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 47) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285361751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285361751 none CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 42, 21, 42, 8, 21, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 48) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285361751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285361751 none CNC(=O)C1(C(=O)N(C)CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 41, 21, 41, 7, 21, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 21, 21, 21, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361751 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361751 Building ZINC001285361769 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361769 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/49 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001285361769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361769 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/50 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001285361769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361769 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361769 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 Building ZINC001285361769 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285361769 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 49) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001285361769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285361769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361769 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 50) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001285361769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285361769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001285361769 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285361769 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285361769 Building ZINC001285396661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/51 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396661 none Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 15, 15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 24, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 51, 49, 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, 41, 52]) total number of confs: 166 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/52 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396661 none Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 17, 17, 17, 17, 17, 17, 12, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 23, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 Building ZINC001285396661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 51) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396661 none Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 15, 15, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 24, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 51, 49, 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, 41, 52]) total number of confs: 166 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 52) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396661 none Cn1cc(CC(=O)N[C@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 17, 17, 17, 17, 17, 17, 12, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 23, 17, 17, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396661 Building ZINC001285396663 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396663 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/53 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396663 none Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 13, 13, 13, 13, 13, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 19, 13, 13, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/54 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396663 none Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 14, 14, 14, 14, 14, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 23, 14, 14, 14, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396663 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 Building ZINC001285396663 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396663 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 53) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396663 none Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 13, 13, 13, 13, 13, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 19, 13, 13, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 54) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396663 none Cn1cc(CC(=O)N[C@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 14, 14, 14, 14, 14, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 23, 14, 14, 14, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396663 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396663 Building ZINC001285396664 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396664 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/55 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396664 none Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 15, 15, 15, 15, 15, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 23, 15, 15, 15, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/56 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396664 none Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 20, 14, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396664 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 Building ZINC001285396664 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396664 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 55) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396664 none Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 23, 23, 15, 15, 15, 15, 15, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 23, 15, 15, 15, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 56) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396664 none Cn1cc(CC(=O)N[C@@H]2CCC[C@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 20, 14, 14, 14, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396664 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396664 Building ZINC001285396666 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396666 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/57 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396666 none Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 19, 19, 19, 19, 19, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 24, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/58 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396666 none Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 16, 16, 16, 16, 16, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 24, 16, 16, 16, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396666 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 Building ZINC001285396666 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285396666 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 57) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285396666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396666 none Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 19, 19, 19, 19, 19, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 24, 19, 19, 19, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 58) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285396666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285396666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285396666 none Cn1cc(CC(=O)N[C@@H]2CCC[C@@H]2CNC(=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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 24, 24, 24, 16, 16, 16, 16, 16, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 24, 16, 16, 16, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285396666 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285396666 Building ZINC001285398380 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398380 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/59 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/59' -> `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]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 21, 21, 28, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/60 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/60' -> `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]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 27, 27, 27, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 27, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398380 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 Building ZINC001285398380 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398380 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 59) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 21, 21, 28, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 60) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 27, 27, 27, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 27, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398380 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398380 Building ZINC001285398382 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398382 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/61 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/61' -> `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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398382 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 28, 28, 28, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 21, 21, 21, 21, 28, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/62 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/62' -> `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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398382 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 20, 20, 25, 25, 25, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 20, 20, 20, 20, 25, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398382 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 Building ZINC001285398382 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398382 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 61) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398382 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 28, 28, 28, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 21, 21, 21, 21, 28, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 62) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398382 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 20, 20, 20, 20, 20, 20, 25, 25, 25, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 20, 20, 20, 20, 25, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398382 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398382 Building ZINC001285398385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/63 `/scratch/xiaobo/3016/xbk-8058097.37/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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398385 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 25, 25, 25, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 21, 21, 25, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/64 `/scratch/xiaobo/3016/xbk-8058097.37/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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398385 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 23, 30, 30, 30, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 23, 23, 23, 23, 30, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 Building ZINC001285398385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 63) grep: /scratch/xiaobo/3016/xbk-8058097.37/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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398385 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 25, 25, 25, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 21, 21, 25, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 64) grep: /scratch/xiaobo/3016/xbk-8058097.37/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]1CCC[C@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398385 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 23, 30, 30, 30, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 23, 23, 23, 23, 30, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398385 Building ZINC001285398387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/65 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/65' -> `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]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398387 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 27, 27, 27, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 20, 20, 27, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/66 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/66' -> `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]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398387 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 22, 22, 29, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 Building ZINC001285398387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 65) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398387 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 27, 27, 27, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 20, 20, 27, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 66) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]n1) `ZINC001285398387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398387 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cc1cc[nH]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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 22, 22, 22, 22, 22, 29, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398387 Building ZINC001285398631 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398631 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/67 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/67' -> `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]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398631 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/68 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/68' -> `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]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398631 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398631 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 Building ZINC001285398631 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398631 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 67) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398631 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 68) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398631 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398631 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398631 Building ZINC001285398635 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398635 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/69 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/69' -> `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]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398635 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/70 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/70' -> `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]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398635 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398635 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 Building ZINC001285398635 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398635 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 69) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398635 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 70) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398635 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398635 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398635 Building ZINC001285398640 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398640 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/71 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/71' -> `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]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398640 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/72 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/72' -> `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]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398640 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398640 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 Building ZINC001285398640 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398640 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 71) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398640 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 72) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)c1nccnc1N) `ZINC001285398640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398640 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398640 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398640 Building ZINC001285398644 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398644 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/73 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/73' -> `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]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398644 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 36, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/74 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/74' -> `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]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398644 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398644 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 Building ZINC001285398644 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285398644 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 73) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285398644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398644 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 36, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 74) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)c1nccnc1N) `ZINC001285398644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285398644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285398644 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=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', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 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, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285398644 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285398644 Building ZINC001285400623 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400623 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/75 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/75' -> `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]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400623 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 5, 5, 5, 5, 5, 5, 8, 14, 14, 14, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 14, 44, 44, 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, 48, 49]) total number of confs: 188 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/76 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/76' -> `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]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400623 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 5, 5, 5, 5, 5, 5, 5, 9, 15, 15, 15, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 15, 42, 42, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400623 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 Building ZINC001285400623 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400623 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 75) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400623 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 5, 5, 5, 5, 5, 5, 8, 14, 14, 14, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 8, 8, 14, 44, 44, 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, 48, 49]) total number of confs: 188 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 76) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400623 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 5, 5, 5, 5, 5, 5, 5, 9, 15, 15, 15, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 15, 42, 42, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400623 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400623 Building ZINC001285400626 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400626 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/77 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/77' -> `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]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 6, 6, 6, 6, 6, 6, 6, 11, 25, 25, 25, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 11, 11, 25, 48, 48, 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, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/78 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/78' -> `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]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 4, 8, 8, 8, 8, 8, 8, 8, 13, 24, 24, 24, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 24, 46, 46, 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, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400626 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 Building ZINC001285400626 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400626 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 77) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 6, 6, 6, 6, 6, 6, 6, 11, 25, 25, 25, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 11, 11, 25, 48, 48, 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, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 78) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1) `ZINC001285400626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 4, 8, 8, 8, 8, 8, 8, 8, 13, 24, 24, 24, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 24, 46, 46, 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, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400626 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400626 Building ZINC001285400630 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400630 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/79 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/79' -> `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]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400630 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 4, 6, 6, 6, 6, 6, 6, 6, 10, 20, 20, 20, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 20, 45, 45, 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, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/80 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/80' -> `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]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400630 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 6, 6, 6, 6, 6, 6, 6, 12, 24, 24, 24, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 12, 12, 24, 44, 44, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400630 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 Building ZINC001285400630 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400630 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 79) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400630 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 4, 6, 6, 6, 6, 6, 6, 6, 10, 20, 20, 20, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 10, 10, 20, 45, 45, 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, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 80) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400630 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 6, 6, 6, 6, 6, 6, 6, 12, 24, 24, 24, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 12, 12, 24, 44, 44, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400630 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400630 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400630 Building ZINC001285400633 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400633 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/81 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/81' -> `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]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 5, 5, 5, 5, 5, 5, 5, 9, 15, 15, 15, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 15, 42, 42, 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, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/82 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/82' -> `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]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 5, 5, 5, 5, 5, 5, 10, 16, 16, 16, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 16, 43, 43, 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, 48, 49]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400633 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 Building ZINC001285400633 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400633 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 81) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 3, 5, 5, 5, 5, 5, 5, 5, 9, 15, 15, 15, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 9, 9, 15, 42, 42, 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, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 82) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1) `ZINC001285400633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 5, 5, 5, 5, 5, 5, 10, 16, 16, 16, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 10, 10, 16, 43, 43, 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, 48, 49]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400633 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400633 Building ZINC001285400661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/83 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 15, 15, 15, 15, 15, 15, 15, 23, 23, 23, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 15, 15, 23, 44, 44, 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, 48, 49]) total number of confs: 183 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/84 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 17, 44, 44, 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, 48, 49]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 Building ZINC001285400661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 83) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 15, 15, 15, 15, 15, 15, 15, 23, 23, 23, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 15, 15, 15, 15, 15, 23, 44, 44, 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, 48, 49]) total number of confs: 183 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 84) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 17, 44, 44, 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, 48, 49]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400661 Building ZINC001285400662 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400662 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/85 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/85' -> `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]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 12, 12, 12, 12, 12, 12, 12, 24, 24, 24, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 12, 12, 12, 12, 24, 41, 41, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/86 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/86' -> `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]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 16, 16, 16, 16, 16, 16, 16, 24, 24, 24, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 24, 47, 47, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400662 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 Building ZINC001285400662 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400662 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 85) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 12, 12, 12, 12, 12, 12, 12, 24, 24, 24, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 12, 12, 12, 12, 24, 41, 41, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 86) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 16, 16, 16, 16, 16, 16, 16, 24, 24, 24, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 24, 47, 47, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400662 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400662 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400662 Building ZINC001285400663 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400663 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/87 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/87' -> `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]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 18, 18, 18, 18, 18, 18, 18, 26, 26, 26, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 18, 18, 18, 18, 18, 26, 48, 48, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/88 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/88' -> `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]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 23, 45, 45, 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, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400663 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 Building ZINC001285400663 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400663 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 87) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 18, 18, 18, 18, 18, 18, 18, 26, 26, 26, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 18, 18, 18, 18, 18, 26, 48, 48, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 88) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1) `ZINC001285400663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 23, 45, 45, 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, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400663 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400663 Building ZINC001285400664 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400664 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/89 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/89' -> `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]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 10, 10, 10, 10, 10, 10, 17, 41, 41, 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, 48, 49]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/90 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/90' -> `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]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 14, 14, 24, 45, 45, 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, 48, 49]) total number of confs: 181 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400664 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 Building ZINC001285400664 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285400664 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 89) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285400664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 10, 10, 10, 10, 10, 10, 17, 41, 41, 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, 48, 49]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 90) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1) `ZINC001285400664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285400664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285400664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1cccn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 14, 14, 24, 45, 45, 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, 48, 49]) total number of confs: 181 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285400664 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285400664 Building ZINC001285401084 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401084 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/91 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401084 none CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 38, 38, 21, 14, 14, 14, 14, 14, 14, 7, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 38, 21, 21, 14, 14, 14, 14, 14, 14, 5, 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: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/92 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401084 none CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 37, 37, 37, 19, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 19, 19, 11, 11, 11, 11, 11, 11, 2, 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: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401084 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 Building ZINC001285401084 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401084 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 91) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401084 none CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 38, 38, 21, 14, 14, 14, 14, 14, 14, 7, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 38, 21, 21, 14, 14, 14, 14, 14, 14, 5, 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: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 92) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401084 none CC(=O)NCC(=O)NC[C@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 37, 37, 37, 19, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 19, 19, 11, 11, 11, 11, 11, 11, 2, 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: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401084 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401084 Building ZINC001285401088 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401088 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/93 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401088 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 37, 37, 20, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 37, 20, 20, 11, 11, 11, 11, 11, 11, 2, 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: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/94 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401088 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 32, 32, 32, 19, 11, 11, 11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 32, 19, 19, 11, 11, 11, 11, 11, 11, 4, 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: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401088 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 Building ZINC001285401088 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401088 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 93) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401088 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 37, 37, 20, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 37, 20, 20, 11, 11, 11, 11, 11, 11, 2, 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: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 94) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401088 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 32, 32, 32, 19, 11, 11, 11, 11, 11, 11, 6, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 32, 19, 19, 11, 11, 11, 11, 11, 11, 4, 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: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401088 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401088 Building ZINC001285401092 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401092 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/95 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401092 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 43, 22, 22, 22, 13, 6, 6, 6, 6, 6, 6, 4, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 22, 13, 13, 6, 6, 6, 6, 6, 6, 3, 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: 215 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/96 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401092 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 21, 21, 21, 13, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 21, 13, 13, 9, 9, 9, 9, 9, 9, 2, 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: 200 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401092 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 Building ZINC001285401092 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401092 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 95) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401092 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 43, 22, 22, 22, 13, 6, 6, 6, 6, 6, 6, 4, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 22, 13, 13, 6, 6, 6, 6, 6, 6, 3, 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: 215 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 96) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401092 none CC(=O)NCC(=O)NC[C@@H]1CCC[C@@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 21, 21, 21, 13, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 21, 13, 13, 9, 9, 9, 9, 9, 9, 2, 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: 200 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401092 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401092 Building ZINC001285401095 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401095 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/97 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401095 none CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 22, 22, 22, 14, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 22, 14, 14, 9, 9, 9, 9, 9, 9, 2, 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: 201 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/98 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401095 none CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 44, 22, 22, 22, 14, 7, 7, 7, 7, 7, 7, 4, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 22, 14, 14, 7, 7, 7, 7, 7, 7, 3, 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: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401095 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 Building ZINC001285401095 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285401095 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 97) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285401095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285401095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401095 none CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 22, 22, 22, 14, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 22, 14, 14, 9, 9, 9, 9, 9, 9, 2, 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: 201 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 98) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285401095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285401095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285401095 none CC(=O)NCC(=O)NC[C@H]1CCC[C@H]1NC(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 44, 22, 22, 22, 14, 7, 7, 7, 7, 7, 7, 4, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 22, 14, 14, 7, 7, 7, 7, 7, 7, 3, 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: 220 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285401095 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285401095 Building ZINC001285402452 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402452 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/99 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402452 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 33, 33, 15, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 15, 15, 7, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/100 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402452 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 32, 32, 18, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 32, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402452 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 Building ZINC001285402452 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402452 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 99) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402452 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 33, 33, 15, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 15, 15, 7, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 100) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402452 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 32, 32, 18, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 32, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402452 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402452 Building ZINC001285402454 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402454 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/101 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402454 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 12, 12, 8, 6, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 39, 12, 8, 8, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/102 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402454 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 12, 12, 12, 9, 3, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 12, 9, 9, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402454 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 Building ZINC001285402454 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402454 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 101) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402454 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 12, 12, 8, 6, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 39, 39, 12, 8, 8, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 102) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402454 none Cn1ccc(CC(=O)NC[C@@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 12, 12, 12, 9, 3, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 12, 9, 9, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402454 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402454 Building ZINC001285402456 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402456 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/103 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402456 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 28, 28, 17, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 28, 17, 17, 7, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/104 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402456 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 33, 33, 17, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402456 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 Building ZINC001285402456 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402456 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 103) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402456 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 28, 28, 17, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 28, 17, 17, 7, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 104) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402456 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 33, 33, 17, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 10, 10, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402456 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402456 Building ZINC001285402458 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402458 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/105 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402458 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 15, 15, 15, 11, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 15, 11, 11, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/106 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402458 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 13, 13, 13, 10, 5, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 13, 10, 10, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402458 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 Building ZINC001285402458 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402458 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 105) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402458 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 15, 15, 15, 11, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 15, 11, 11, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 106) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285402458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285402458 none Cn1ccc(CC(=O)NC[C@H]2CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 13, 13, 13, 10, 5, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 13, 10, 10, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402458 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402458 Building ZINC001285402577 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402577 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/107 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/107' -> `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]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 9, 13, 13, 13, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 9, 9, 13, 41, 41, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/108 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/108' -> `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]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 4, 4, 4, 4, 4, 8, 14, 14, 14, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 8, 8, 14, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402577 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 Building ZINC001285402577 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402577 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 107) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 9, 13, 13, 13, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 9, 9, 13, 41, 41, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 108) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 4, 4, 4, 4, 4, 8, 14, 14, 14, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 8, 8, 14, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402577 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402577 Building ZINC001285402579 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402579 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/109 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/109' -> `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]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402579 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 4, 4, 4, 4, 4, 10, 18, 18, 18, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 10, 10, 18, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/110 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/110' -> `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]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402579 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 8, 12, 12, 12, 38, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 8, 8, 12, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402579 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 Building ZINC001285402579 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402579 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 109) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402579 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 4, 4, 4, 4, 4, 10, 18, 18, 18, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 10, 10, 18, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 110) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402579 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 8, 12, 12, 12, 38, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 8, 8, 12, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402579 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402579 Building ZINC001285402581 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402581 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/111 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/111' -> `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]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402581 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 16, 16, 23, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/112 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/112' -> `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]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402581 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 22, 22, 22, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 22, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402581 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 Building ZINC001285402581 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402581 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 111) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402581 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 16, 16, 23, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 112) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402581 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 22, 22, 22, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 22, 43, 43, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([9, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402581 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402581 Building ZINC001285402583 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402583 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/113 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/113' -> `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]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402583 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 14, 25, 25, 25, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 14, 14, 25, 46, 46, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/114 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/114' -> `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]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402583 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 25, 25, 25, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 15, 15, 25, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402583 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 Building ZINC001285402583 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285402583 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 113) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285402583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402583 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 6, 6, 14, 25, 25, 25, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 14, 14, 25, 46, 46, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 114) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]n1) `ZINC001285402583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285402583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285402583 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCC[C@@H]1CNC(=O)Cc1cc[nH]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', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 25, 25, 25, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 15, 15, 25, 48, 48, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285402583 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285402583 Building ZINC001285403177 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403177 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/115 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/115' -> `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]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 46, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 13, 13, 23, 46, 46, 48, 48, 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/116 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/116' -> `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]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 42, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 14, 14, 23, 42, 42, 43, 43, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403177 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 Building ZINC001285403177 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403177 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 115) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 46, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 13, 13, 23, 46, 46, 48, 48, 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 116) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 42, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 14, 14, 14, 14, 23, 42, 42, 43, 43, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403177 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403177 Building ZINC001285403179 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403179 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/117 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/117' -> `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]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 16, 16, 16, 16, 16, 25, 25, 25, 43, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 25, 43, 43, 45, 45, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/118 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/118' -> `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]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 39, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 17, 17, 17, 17, 23, 39, 39, 41, 41, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403179 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 Building ZINC001285403179 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403179 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 117) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 16, 16, 16, 16, 16, 25, 25, 25, 43, 45, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 25, 43, 43, 45, 45, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 118) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 39, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 17, 17, 17, 17, 23, 39, 39, 41, 41, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403179 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403179 Building ZINC001285403181 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403181 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/119 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/119' -> `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]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403181 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 49, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 33, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/120 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/120' -> `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]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403181 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 19, 19, 19, 25, 25, 25, 38, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 19, 19, 19, 19, 19, 25, 38, 38, 41, 41, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403181 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 Building ZINC001285403181 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403181 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 119) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403181 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 49, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 33, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 120) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1) `ZINC001285403181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403181 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 19, 19, 19, 25, 25, 25, 38, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 19, 19, 19, 19, 19, 25, 38, 38, 41, 41, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403181 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403181 Building ZINC001285403183 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403183 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/121 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/121' -> `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]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403183 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 15, 25, 25, 25, 47, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 25, 47, 47, 48, 48, 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]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/122 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/122' -> `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]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403183 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 12, 12, 12, 12, 12, 12, 23, 23, 23, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 23, 40, 40, 40, 40, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403183 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 Building ZINC001285403183 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285403183 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 121) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285403183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403183 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 15, 25, 25, 25, 47, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 25, 47, 47, 48, 48, 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]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 122) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1) `ZINC001285403183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285403183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285403183 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)CCn1cncn1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 12, 12, 12, 12, 12, 12, 23, 23, 23, 40, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 23, 40, 40, 40, 40, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285403183 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285403183 Building ZINC001285410377 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410377 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/123 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/123' -> `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]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 16, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 16, 36, 36, 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, 48, 49]) total number of confs: 176 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/124 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/124' -> `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]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 17, 36, 36, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410377 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 Building ZINC001285410377 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410377 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 123) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 16, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 16, 36, 36, 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, 48, 49]) total number of confs: 176 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 124) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 17, 36, 36, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410377 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410377 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410377 Building ZINC001285410378 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410378 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/125 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/125' -> `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]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410378 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 20, 20, 20, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 20, 40, 40, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/126 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/126' -> `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]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410378 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 18, 38, 38, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410378 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 Building ZINC001285410378 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410378 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 125) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410378 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 20, 20, 20, 40, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 20, 40, 40, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 126) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410378 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 18, 38, 38, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410378 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410378 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410378 Building ZINC001285410379 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410379 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/127 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/127' -> `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]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410379 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 12, 12, 19, 38, 38, 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, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/128 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/128' -> `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]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410379 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 19, 34, 34, 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, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410379 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 Building ZINC001285410379 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410379 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 127) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410379 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 12, 12, 19, 38, 38, 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, 48, 49]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 128) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1) `ZINC001285410379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410379 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 7, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 19, 34, 34, 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, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410379 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410379 Building ZINC001285410380 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410380 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/129 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/129' -> `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]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 15, 34, 34, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/130 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/130' -> `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]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 16, 31, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 16, 31, 31, 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, 48, 49]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410380 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 Building ZINC001285410380 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285410380 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 129) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285410380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 5, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 15, 34, 34, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 130) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1) `ZINC001285410380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285410380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285410380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)Cn1ccnc1 NO_LONG_NAME dock 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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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, 9, 13, 13, 13, 13, 13, 13, 13, 16, 16, 16, 31, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 16, 31, 31, 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, 48, 49]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285410380 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285410380 Building ZINC001285416715 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416715 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/131 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/131' -> `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]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416715 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 23, 30, 30, 30, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 23, 23, 30, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/132 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/132' -> `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]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416715 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 27, 27, 36, 36, 36, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 27, 27, 27, 27, 36, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416715 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 Building ZINC001285416715 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416715 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 131) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416715 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 23, 23, 30, 30, 30, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 23, 23, 30, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 132) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416715 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 27, 27, 36, 36, 36, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 27, 27, 27, 27, 36, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416715 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416715 Building ZINC001285416719 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416719 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/133 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/133' -> `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]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416719 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 48, 50, 50, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 22, 22, 22, 22, 35, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 166 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/134 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/134' -> `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]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416719 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 35, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416719 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 Building ZINC001285416719 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416719 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 133) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416719 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 48, 50, 50, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 22, 22, 22, 22, 35, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 166 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 134) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416719 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 35, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416719 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416719 Building ZINC001285416722 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416722 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/135 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/135' -> `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]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 25, 34, 34, 34, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 25, 25, 25, 25, 25, 34, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/136 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/136' -> `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]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 25, 32, 32, 32, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 25, 25, 25, 25, 25, 25, 32, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416722 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 Building ZINC001285416722 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416722 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 135) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 25, 34, 34, 34, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 25, 25, 25, 25, 25, 34, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 136) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 25, 25, 25, 25, 32, 32, 32, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 25, 25, 25, 25, 25, 25, 32, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416722 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416722 Building ZINC001285416724 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416724 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/137 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/137' -> `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]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416724 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 32, 32, 32, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 32, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/138 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/138' -> `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]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416724 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 33, 33, 33, 48, 50, 50, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 33, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416724 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 Building ZINC001285416724 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285416724 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 137) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285416724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416724 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 22, 22, 32, 32, 32, 46, 50, 50, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 32, 50, 50, 46, 46, 46, 46] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 138) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(C(N)=O)CC1) `ZINC001285416724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285416724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285416724 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC[C@H]1NC(=O)C1(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 33, 33, 33, 48, 50, 50, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 21, 21, 21, 21, 21, 21, 33, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285416724 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285416724 Building ZINC001285420140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/139 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/139' -> `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]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/140 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/140' -> `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]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/141 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/141' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 26, 50, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/142 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/142' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 Building ZINC001285420140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 139) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 140) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 141) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 26, 50, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 142) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 Building ZINC001285420140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 139) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 140) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 141) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 26, 50, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 142) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 Building ZINC001285420140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 139) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 140) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 141) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 26, 50, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 142) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1) `ZINC001285420140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420140 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 27, 27, 27, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 50, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420140 Building ZINC001285420712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/143 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/143' -> `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]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 31, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/144 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/144' -> `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]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/145 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/145' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/146 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/146' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 Building ZINC001285420712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 143) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 31, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 144) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 145) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 146) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 Building ZINC001285420712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 143) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 31, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 144) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 145) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 146) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 Building ZINC001285420712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285420712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 143) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 31, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 144) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 145) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 146) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1) `ZINC001285420712.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285420712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285420712 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[C@@H](NC(=O)c2ncn(C)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 5, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 32, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 32, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285420712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285420712 Building ZINC001285424711 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424711 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/147 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424711 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 268 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/148 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424711 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 21, 21, 21, 17, 10, 9, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 17, 17, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 235 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424711 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 Building ZINC001285424711 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424711 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 147) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424711 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 268 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 148) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424711 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 21, 21, 21, 17, 10, 9, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 17, 17, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 235 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424711 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424711 Building ZINC001285424712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/149 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424712 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 252 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/150 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424712 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 24, 24, 24, 19, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 24, 19, 19, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 254 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 Building ZINC001285424712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 149) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424712 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 252 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 150) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424712 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 24, 24, 24, 19, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 24, 19, 19, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 254 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424712 Building ZINC001285424713 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424713 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/151 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424713 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 24, 24, 24, 19, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 24, 19, 19, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 254 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/152 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424713 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 252 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424713 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 Building ZINC001285424713 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424713 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 151) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424713 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 24, 24, 24, 19, 10, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 24, 19, 19, 30, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 254 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 152) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424713 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 252 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424713 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424713 Building ZINC001285424714 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424714 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/153 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424714 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 21, 21, 21, 17, 10, 9, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 17, 17, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 235 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/154 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424714 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 268 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424714 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 Building ZINC001285424714 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285424714 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 153) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285424714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424714 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 21, 21, 21, 17, 10, 9, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 17, 17, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 235 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 154) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1) `ZINC001285424714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285424714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285424714 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1cccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 50, 23, 23, 23, 18, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 23, 18, 18, 33, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 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]) total number of confs: 268 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285424714 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285424714 Building ZINC001285425173 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285425173 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/155 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285425173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425173 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 18, 26, 26, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/156 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285425173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425173 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 14, 14, 14, 24, 31, 31, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 42, 24, 24, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285425173 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 Building ZINC001285425173 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285425173 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 155) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285425173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425173 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 18, 26, 26, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 156) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285425173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425173 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 14, 14, 14, 24, 31, 31, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 42, 24, 24, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285425173 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425173 Building ZINC001285425176 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285425176 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/157 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285425176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425176 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 16, 16, 16, 22, 29, 29, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 48, 22, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 237 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/158 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285425176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425176 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 16, 22, 22, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 16, 16, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285425176 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 Building ZINC001285425176 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285425176 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 157) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285425176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425176 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 16, 16, 16, 22, 29, 29, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 48, 22, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 237 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 158) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(F)CCCCC1) `ZINC001285425176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285425176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285425176 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(F)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 16, 22, 22, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 16, 16, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285425176 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285425176 Building ZINC001285426041 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426041 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/159 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/160 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/161 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/161' -> `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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/162 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/162' -> `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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426041 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 Building ZINC001285426041 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426041 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 159) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 160) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 161) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 162) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426041 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 Building ZINC001285426041 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426041 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 159) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 160) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 161) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 162) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426041 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 Building ZINC001285426041 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426041 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 159) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 160) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 161) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 18, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 162) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426041 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426041 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426041 Building ZINC001285426042 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426042 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/163 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/163' -> `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](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/164 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/164' -> `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](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/165 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/165' -> `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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/166 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/166' -> `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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426042 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 Building ZINC001285426042 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426042 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 163) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 164) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 165) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 166) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426042 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 Building ZINC001285426042 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426042 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 163) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 164) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 165) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 166) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426042 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 Building ZINC001285426042 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285426042 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 163) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 164) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](F)CC1) `ZINC001285426042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 165) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 17, 24, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 24, 17, 17, 24, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 212 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 166) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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](O)CNC(=O)[C@H]1CC[C@@H](F)CC1) `ZINC001285426042.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285426042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@H]1CC[C@@H](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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 18, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426042 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426042 Building ZINC001285426087 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426087 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/167 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285426087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285426087 none CCOCC1(C(=O)NC[C@H](O)CNC(=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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 18, 18, 18, 13, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 49, 49, 18, 13, 13, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/168 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285426087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285426087 none CCOCC1(C(=O)NC[C@H](O)CNC(=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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 38, 16, 16, 16, 11, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 48, 48, 16, 11, 11, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426087 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 Building ZINC001285426087 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426087 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 167) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCOCC1(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285426087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285426087 none CCOCC1(C(=O)NC[C@H](O)CNC(=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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 18, 18, 18, 13, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 49, 49, 18, 13, 13, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 168) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCOCC1(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285426087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285426087 none CCOCC1(C(=O)NC[C@H](O)CNC(=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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 38, 16, 16, 16, 11, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 48, 48, 16, 11, 11, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426087 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426087 Building ZINC001285426061 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426061 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/169 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426061 none CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 34, 34, 34, 34, 22, 22, 22, 19, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 34, 34, 22, 19, 19, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/170 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426061 none CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 37, 37, 37, 37, 23, 23, 23, 17, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 23, 17, 17, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426061 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 Building ZINC001285426061 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426061 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 169) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426061 none CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 34, 34, 34, 34, 22, 22, 22, 19, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 34, 34, 22, 19, 19, 30, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 246 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 170) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426061 none CCc1cncc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 37, 37, 37, 37, 23, 23, 23, 17, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 23, 17, 17, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426061 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426061 Building ZINC001285426062 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426062 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/171 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426062 none CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 37, 37, 37, 37, 23, 23, 23, 17, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 23, 17, 17, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/172 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426062 none CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 35, 35, 23, 23, 23, 20, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 23, 20, 20, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 246 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426062 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 Building ZINC001285426062 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426062 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 171) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426062 none CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 37, 37, 37, 37, 23, 23, 23, 17, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 23, 17, 17, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 172) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285426062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285426062 none CCc1cncc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 35, 35, 23, 23, 23, 20, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 23, 20, 20, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 246 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426062 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426062 Building ZINC001285426089 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426089 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/173 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426089 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 7, 10, 10, 10, 31, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 12, 7, 7, 10, 50, 50, 50, 50, 31, 31, 31, 31] 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/174 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426089 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 15, 15, 15, 40, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 15, 50, 50, 50, 50, 40, 40, 40, 40] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426089 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 Building ZINC001285426089 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426089 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 173) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426089 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 7, 10, 10, 10, 31, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 12, 7, 7, 10, 50, 50, 50, 50, 31, 31, 31, 31] 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 174) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426089 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 15, 15, 15, 40, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 15, 50, 50, 50, 50, 40, 40, 40, 40] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426089 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426089 Building ZINC001285426090 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426090 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/175 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426090 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 15, 15, 15, 40, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 15, 50, 50, 50, 50, 40, 40, 40, 40] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/176 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426090 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 14, 14, 14, 43, 50, 50, 50, 50, 50, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 10, 10, 14, 50, 50, 50, 50, 43, 43, 43, 43] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426090 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 Building ZINC001285426090 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426090 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 175) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426090 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 13, 15, 15, 15, 40, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 27, 13, 13, 15, 50, 50, 50, 50, 40, 40, 40, 40] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 176) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC[C@H](O)CNC(=O)C1(c2cccnc2)CC1) `ZINC001285426090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426090 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1(c2cccnc2)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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 14, 14, 14, 43, 50, 50, 50, 50, 50, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 10, 10, 14, 50, 50, 50, 50, 43, 43, 43, 43] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426090 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426090 Building ZINC001285426235 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426235 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/177 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/177' -> `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](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 17, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 17, 17, 24, 50, 50, 50] 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: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/178 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/178' -> `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](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 11, 11, 11, 19, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 21, 50, 50, 50] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426235 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 Building ZINC001285426235 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426235 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 177) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 17, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 17, 17, 24, 50, 50, 50] 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: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 178) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 11, 11, 11, 19, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 21, 50, 50, 50] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426235 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426235 Building ZINC001285426236 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426236 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/179 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/179' -> `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](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426236 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 11, 11, 11, 19, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 21, 50, 50, 50] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/180 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/180' -> `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](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426236 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 17, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 17, 17, 23, 50, 50, 50] 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: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426236 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 Building ZINC001285426236 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426236 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 179) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426236 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 11, 11, 11, 19, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 19, 19, 21, 50, 50, 50] 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 180) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1) `ZINC001285426236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426236 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 17, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 17, 17, 23, 50, 50, 50] 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: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426236 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426236 Building ZINC001285426471 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426471 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/181 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426471 none Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/182 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426471 none Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 291 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426471 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 Building ZINC001285426471 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426471 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 181) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426471 none Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 182) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426471 none Cc1ncsc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 26, 11, 26, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 33, 33, 78, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 291 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426471 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426471 Building ZINC001285426472 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426472 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/183 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426472 none Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/184 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426472 none Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426472 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 Building ZINC001285426472 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426472 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 183) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426472 none Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 184) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285426472 none Cc1ncsc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 14, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 32, 27, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426472 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426472 Building ZINC001285426533 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426533 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/185 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/185' -> `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](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 23, 23, 22, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 69, 32, 32, 47, 50, 50, 50, 50] 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]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/186 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/186' -> `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](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 26, 38, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 78, 38, 38, 49, 50, 50, 50, 50] 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]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426533 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 Building ZINC001285426533 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426533 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 185) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 23, 23, 22, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 69, 32, 32, 47, 50, 50, 50, 50] 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]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 186) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 26, 38, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 78, 38, 38, 49, 50, 50, 50, 50] 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]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426533 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426533 Building ZINC001285426534 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426534 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/187 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426534 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 26, 38, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 78, 38, 38, 49, 50, 50, 50, 50] 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]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/188 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426534 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 23, 23, 22, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 69, 32, 32, 47, 50, 50, 50, 50] 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]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426534 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 Building ZINC001285426534 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426534 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 187) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426534 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 26, 26, 26, 38, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 78, 38, 38, 49, 50, 50, 50, 50] 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]) total number of confs: 297 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 188) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1) `ZINC001285426534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426534 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cc2ncccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 23, 23, 22, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 69, 32, 32, 47, 50, 50, 50, 50] 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]) total number of confs: 271 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426534 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426534 Building ZINC001285426557 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426557 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/189 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426557 none COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 22, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 208 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/190 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426557 none COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 20, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 20, 20, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426557 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 Building ZINC001285426557 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426557 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 189) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426557 none COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 22, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 22, 22, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 208 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 190) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426557 none COc1ccccc1C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 20, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 20, 20, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426557 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426557 Building ZINC001285426558 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426558 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/191 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426558 none COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 20, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 20, 20, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/192 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426558 none COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 23, 18, 9, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 23, 23, 54, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426558 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 Building ZINC001285426558 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426558 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 191) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426558 none COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 20, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 20, 20, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 192) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426558 none COc1ccccc1C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 23, 18, 9, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 23, 23, 54, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426558 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426558 Building ZINC001285426571 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426571 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/193 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426571 none CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 18, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/194 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426571 none CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 16, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 16, 16, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426571 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 Building ZINC001285426571 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426571 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 193) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426571 none CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 35, 18, 15, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 194) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426571 none CC1=C(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 16, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 16, 16, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426571 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426571 Building ZINC001285426572 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426572 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/195 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426572 none CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 17, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/196 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426572 none CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 17, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426572 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 Building ZINC001285426572 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426572 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 195) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426572 none CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 17, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 39, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 196) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1) `ZINC001285426572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285426572 none CC1=C(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 31, 31, 17, 14, 10, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426572 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426572 Building ZINC001285426593 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426593 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/197 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/197' -> `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](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426593 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 15, 15, 15, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 21, 21, 25, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/198 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/198' -> `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](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426593 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 12, 12, 12, 19, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 19, 19, 27, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426593 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 Building ZINC001285426593 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426593 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 197) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426593 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 15, 15, 15, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 21, 21, 25, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 198) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426593 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 12, 12, 12, 19, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 19, 19, 27, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426593 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426593 Building ZINC001285426594 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426594 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/199 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/199' -> `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](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426594 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 12, 12, 12, 18, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 18, 18, 26, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/200 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/200' -> `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](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426594 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 15, 15, 15, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 21, 21, 25, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426594 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 Building ZINC001285426594 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426594 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 199) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426594 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 12, 12, 12, 18, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 18, 18, 26, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 200) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1) `ZINC001285426594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285426594 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2n[nH]cc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 15, 15, 15, 21, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 45, 21, 21, 25, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426594 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426594 Building ZINC001285426813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/201 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426813 none Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 40, 11, 11, 11, 6, 6, 5, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 11, 6, 6, 18, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/202 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426813 none Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 43, 10, 10, 10, 8, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 10, 8, 8, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 Building ZINC001285426813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 201) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426813 none Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 40, 11, 11, 11, 6, 6, 5, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 11, 6, 6, 18, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 202) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426813 none Cc1cnccc1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 43, 10, 10, 10, 8, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 10, 8, 8, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426813 Building ZINC001285426814 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426814 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/203 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426814 none Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 42, 10, 10, 10, 8, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 10, 8, 8, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/204 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426814 none Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 50, 50, 40, 11, 11, 11, 6, 6, 5, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 11, 6, 6, 18, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426814 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 Building ZINC001285426814 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285426814 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 203) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285426814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285426814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426814 none Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 50, 50, 42, 10, 10, 10, 8, 8, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 10, 8, 8, 24, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 204) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285426814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285426814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285426814 none Cc1cnccc1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 50, 50, 40, 11, 11, 11, 6, 6, 5, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 11, 6, 6, 18, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285426814 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285426814 Building ZINC001285427153 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427153 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/205 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427153 none CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 40, 40, 40, 26, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 40, 26, 26, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/206 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427153 none CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 23, 17, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 23, 23, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427153 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 Building ZINC001285427153 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427153 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 205) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427153 none CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 40, 40, 40, 26, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 40, 26, 26, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 206) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427153 none CCc1oc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 23, 17, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 23, 23, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427153 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427153 Building ZINC001285427154 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427154 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/207 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427154 none CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 23, 17, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 23, 23, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/208 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427154 none CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 40, 40, 40, 27, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 40, 27, 27, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 267 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427154 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 Building ZINC001285427154 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427154 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 207) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427154 none CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 23, 17, 11, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 23, 23, 51, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 208) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C) `ZINC001285427154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427154 none CCc1oc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 40, 40, 40, 27, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 40, 27, 27, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 267 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427154 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427154 Building ZINC001285427161 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427161 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/209 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427161 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 11, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 11, 11, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 240 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/210 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427161 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 43, 48, 14, 14, 14, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 43, 43, 14, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 239 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427161 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 Building ZINC001285427161 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427161 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 209) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427161 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 11, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 11, 11, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 240 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 210) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427161 none C[C@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 43, 48, 14, 14, 14, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 43, 43, 14, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 239 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427161 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427161 Building ZINC001285427162 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427162 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/211 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427162 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 42, 48, 14, 14, 14, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 42, 42, 14, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/212 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427162 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 11, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 11, 11, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 240 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427162 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 Building ZINC001285427162 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427162 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 211) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427162 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 42, 48, 14, 14, 14, 12, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 42, 42, 14, 12, 12, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 212) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427162 none C[C@@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 11, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 11, 11, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 240 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427162 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427162 Building ZINC001285427163 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427163 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/213 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427163 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 16, 16, 16, 13, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 16, 13, 13, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/214 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427163 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 43, 49, 16, 16, 16, 12, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 43, 43, 16, 12, 12, 21, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 243 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427163 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 Building ZINC001285427163 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427163 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 213) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427163 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 16, 16, 16, 13, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 16, 13, 13, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 214) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427163 none C[C@@H](CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 43, 49, 16, 16, 16, 12, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 43, 43, 16, 12, 12, 21, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 243 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427163 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427163 Building ZINC001285427164 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427164 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/215 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427164 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 12, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 12, 12, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/216 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427164 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 16, 16, 16, 13, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 16, 13, 13, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427164 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 Building ZINC001285427164 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427164 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 215) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427164 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 15, 15, 15, 12, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 15, 12, 12, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 216) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1) `ZINC001285427164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427164 none C[C@H](CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 49, 16, 16, 16, 13, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 49, 49, 49, 42, 42, 16, 13, 13, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 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]) total number of confs: 242 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427164 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427164 Building ZINC001285427183 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427183 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/217 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427183 none CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 25, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 38, 25, 25, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/218 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427183 none CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 41, 41, 41, 27, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 41, 27, 27, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427183 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 Building ZINC001285427183 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427183 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 217) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427183 none CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 25, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 38, 25, 25, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 218) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427183 none CCc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 41, 41, 41, 27, 14, 9, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 41, 27, 27, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427183 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427183 Building ZINC001285427184 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427184 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/219 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427184 none CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 25, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 25, 25, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/220 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427184 none CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 25, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 38, 25, 25, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427184 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 Building ZINC001285427184 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427184 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 219) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427184 none CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 37, 37, 37, 25, 13, 9, 13, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50, 50, 37, 25, 25, 39, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 220) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1) `ZINC001285427184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285427184 none CCc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 25, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 38, 25, 25, 45, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 277 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427184 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427184 Building ZINC001285427197 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427197 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/221 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427197 none Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 35, 26, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/222 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427197 none Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 28, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427197 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 Building ZINC001285427197 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427197 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 221) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427197 none Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 35, 26, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 81, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 222) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427197 none Cc1nc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 28, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427197 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427197 Building ZINC001285427198 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427198 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/223 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427198 none Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 28, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/224 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427198 none Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 27, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 36, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 304 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427198 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 Building ZINC001285427198 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427198 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 223) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427198 none Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 28, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 224) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C) `ZINC001285427198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427198 none Cc1nc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)sc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 14, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 27, 11, 28, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 36, 84, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 304 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427198 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427198 Building ZINC001285427249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/225 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427249 none Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 19, 43, 43, 19, 19, 14, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 43, 19, 14, 14, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/226 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427249 none Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 22, 45, 45, 22, 22, 15, 10, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 15, 15, 30, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 Building ZINC001285427249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 225) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427249 none Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 19, 43, 43, 19, 19, 14, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 43, 19, 14, 14, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 226) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427249 none Cc1ccc([C@@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 22, 45, 45, 22, 22, 15, 10, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 15, 15, 30, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 245 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427249 Building ZINC001285427250 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427250 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/227 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427250 none Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 22, 45, 45, 22, 22, 15, 9, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 15, 15, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/228 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427250 none Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 19, 43, 43, 19, 19, 14, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 43, 19, 14, 14, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427250 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 Building ZINC001285427250 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427250 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 227) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427250 none Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 45, 22, 45, 45, 22, 22, 15, 9, 5, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 22, 15, 15, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 228) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427250 none Cc1ccc([C@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 19, 43, 43, 19, 19, 14, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 43, 19, 14, 14, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427250 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427250 Building ZINC001285427251 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427251 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/229 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427251 none Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 24, 47, 47, 24, 24, 17, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 24, 17, 17, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/230 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427251 none Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 22, 46, 46, 22, 22, 14, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 46, 22, 14, 14, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427251 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 Building ZINC001285427251 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427251 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 229) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427251 none Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 24, 47, 47, 24, 24, 17, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 24, 17, 17, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 230) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427251 none Cc1ccc([C@H](C)C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 46, 22, 46, 46, 22, 22, 14, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 46, 22, 14, 14, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427251 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427251 Building ZINC001285427252 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427252 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/231 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427252 none Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 22, 47, 47, 22, 22, 14, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 22, 14, 14, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/232 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427252 none Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 25, 47, 47, 25, 25, 16, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 25, 16, 16, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427252 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 Building ZINC001285427252 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427252 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 231) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427252 none Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 22, 47, 47, 22, 22, 14, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 22, 14, 14, 24, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 232) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427252 none Cc1ccc([C@@H](C)C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 25, 47, 47, 25, 25, 16, 11, 9, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 47, 47, 25, 16, 16, 33, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427252 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427252 Building ZINC001285427255 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427255 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/233 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427255 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/234 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427255 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 7, 12, 12, 12, 20, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 36, 20, 20, 24, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427255 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 Building ZINC001285427255 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427255 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 233) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427255 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 234) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427255 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 7, 12, 12, 12, 20, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 36, 20, 20, 24, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427255 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427255 Building ZINC001285427256 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427256 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/235 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/236 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427256 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 Building ZINC001285427256 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427256 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 235) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 236) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2) `ZINC001285427256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1ccc2c(c1)COC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 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] 1 hydrogens need rotated 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, 11, 11, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427256 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427256 Building ZINC001285427385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/237 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285427385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427385 none Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 9, 9, 9, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 9, 5, 5, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/238 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285427385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427385 none Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 34, 10, 10, 10, 8, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 10, 8, 8, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 Building ZINC001285427385 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427385 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 237) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285427385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427385 none Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 9, 9, 9, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 9, 5, 5, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 238) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285427385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427385 none Cc1noc(C)c1CC(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 34, 10, 10, 10, 8, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 10, 8, 8, 24, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427385 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427385 Building ZINC001285427386 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427386 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/239 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285427386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427386 none Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 11, 11, 11, 9, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 11, 9, 9, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/240 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285427386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427386 none Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 9, 9, 9, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 9, 5, 5, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427386 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 Building ZINC001285427386 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427386 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 239) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285427386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427386 none Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 11, 11, 11, 9, 9, 7, 9, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 11, 9, 9, 27, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 240) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285427386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285427386 none Cc1noc(C)c1CC(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in 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, 32, 9, 9, 9, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 9, 5, 5, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427386 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427386 Building ZINC001285427391 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427391 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/241 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427391 none Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 26, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 255 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/242 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427391 none Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 48, 48, 31, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 31, 31, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427391 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 Building ZINC001285427391 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427391 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 241) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427391 none Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 26, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 63, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 255 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 242) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427391 none Cc1nc(C)c(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 48, 48, 31, 23, 12, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 31, 31, 69, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427391 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427391 Building ZINC001285427392 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427392 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/243 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427392 none Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 31, 24, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 72, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/244 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427392 none Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 26, 20, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 60, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427392 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 Building ZINC001285427392 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427392 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 243) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427392 none Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 31, 24, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 31, 31, 72, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 244) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1) `ZINC001285427392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285427392 none Cc1nc(C)c(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 26, 20, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 60, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427392 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427392 Building ZINC001285427413 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427413 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/245 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427413 none Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 31, 31, 29, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 31, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/246 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427413 none Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 34, 34, 29, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427413 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 Building ZINC001285427413 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427413 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 245) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427413 none Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 31, 31, 29, 15, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 31, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 246) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427413 none Cc1cc(C(=O)NC[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 34, 34, 29, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427413 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427413 Building ZINC001285427414 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427414 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/247 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427414 none Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 34, 34, 29, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/248 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427414 none Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 32, 32, 30, 16, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 30, 30, 51, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427414 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 Building ZINC001285427414 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427414 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 247) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427414 none Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 34, 34, 29, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 29, 29, 48, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 248) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1) `ZINC001285427414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285427414 none Cc1cc(C(=O)NC[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 32, 32, 30, 16, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 32, 30, 30, 51, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427414 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427414 Building ZINC001285427466 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427466 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/249 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/249' -> `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](O)CNC(=O)CC1CCOCC1) `ZINC001285427466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427466 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 13, 13, 13, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 13, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/250 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/250' -> `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](O)CNC(=O)CC1CCOCC1) `ZINC001285427466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427466 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 7, 12, 12, 12, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 12, 7, 7, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427466 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 Building ZINC001285427466 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427466 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 249) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1) `ZINC001285427466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427466 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 9, 13, 13, 13, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 18, 9, 9, 13, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 250) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1) `ZINC001285427466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427466 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 7, 12, 12, 12, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 12, 7, 7, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427466 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427466 Building ZINC001285427468 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427468 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/251 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/251' -> `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](O)CNC(=O)CC1CCOCC1) `ZINC001285427468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427468 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 14, 14, 14, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 14, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/252 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/252' -> `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](O)CNC(=O)CC1CCOCC1) `ZINC001285427468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427468 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 9, 9, 13, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427468 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 Building ZINC001285427468 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427468 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 251) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1) `ZINC001285427468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427468 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 14, 14, 14, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 14, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 252) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1) `ZINC001285427468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427468 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 21, 9, 9, 13, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427468 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427468 Building ZINC001285427622 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427622 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/253 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/253' -> `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](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427622 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 14, 14, 13, 20, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/254 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/254' -> `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](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427622 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 16, 16, 16, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427622 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 Building ZINC001285427622 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427622 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 253) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427622 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 14, 14, 13, 20, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 254) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427622 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 16, 16, 16, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 48, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427622 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427622 Building ZINC001285427625 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427625 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/255 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/255' -> `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](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427625 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 17, 17, 17, 22, 31, 31, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 51, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/256 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/256' -> `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](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427625 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 15, 15, 14, 21, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427625 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 Building ZINC001285427625 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427625 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 255) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427625 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 17, 17, 17, 22, 31, 31, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 51, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 256) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1) `ZINC001285427625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427625 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C1Cc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 15, 15, 14, 21, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 45, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427625 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427625 Building ZINC001285427963 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427963 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/257 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/257' -> `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](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427963 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 22, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 66, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/258 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/258' -> `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](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427963 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 81, 37, 37, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427963 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 Building ZINC001285427963 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427963 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 257) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427963 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 22, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 66, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 258) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427963 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 81, 37, 37, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427963 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427963 Building ZINC001285427966 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427966 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/259 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/259' -> `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](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427966 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 81, 37, 37, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/260 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/260' -> `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](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427966 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 22, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 66, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427966 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 Building ZINC001285427966 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427966 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 259) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427966 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 27, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 81, 37, 37, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 260) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]c2ccccc21) `ZINC001285427966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427966 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1n[nH]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', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 22, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 66, 36, 36, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427966 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427966 Building ZINC001285427985 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427985 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/261 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/261' -> `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](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427985 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 16, 16, 16, 40, 40, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 16, 40, 40, 40, 40, 40, 40, 50, 50, 50, 50] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/262 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/262' -> `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](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427985 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 17, 17, 17, 36, 36, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 12, 12, 17, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50] 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, 51]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427985 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 Building ZINC001285427985 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427985 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 261) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427985 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 9, 16, 16, 16, 40, 40, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 9, 9, 16, 40, 40, 40, 40, 40, 40, 50, 50, 50, 50] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 262) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427985 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 17, 17, 17, 36, 36, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 12, 12, 17, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50] 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, 51]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427985 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427985 Building ZINC001285427988 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427988 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/263 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/263' -> `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](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427988 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 17, 17, 17, 38, 38, 38, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 12, 12, 17, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50] 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, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/264 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/264' -> `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](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427988 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 17, 17, 17, 41, 41, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 10, 10, 17, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427988 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 Building ZINC001285427988 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285427988 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 263) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285427988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427988 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 17, 17, 17, 38, 38, 38, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 24, 12, 12, 17, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50] 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, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 264) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1) `ZINC001285427988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285427988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285427988 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)C(C)(C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 5, 5, 5, 10, 17, 17, 17, 41, 41, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 15, 10, 10, 17, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285427988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285427988 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285427988 Building ZINC001285428067 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428067 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/265 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/265' -> `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](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428067 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 11, 16, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 16, 16, 29, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/266 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/266' -> `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](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428067 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 18, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 18, 18, 30, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428067 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 Building ZINC001285428067 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428067 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 265) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428067 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 11, 11, 11, 16, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 16, 16, 29, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 266) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428067 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 18, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 18, 18, 30, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428067 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428067 Building ZINC001285428072 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428072 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/267 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/267' -> `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](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 18, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 18, 18, 30, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/268 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/268' -> `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](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 17, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 17, 17, 28, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428072 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 Building ZINC001285428072 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428072 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 267) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 18, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 18, 18, 30, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 268) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21) `ZINC001285428072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cncc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.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, 7, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 12, 12, 17, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 17, 17, 28, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428072 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428072 Building ZINC001285428311 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428311 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/269 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/269' -> `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](O)CNC(=O)c1scnc1Cl) `ZINC001285428311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428311 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 20, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 20, 20, 28, 50] 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]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/270 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/270' -> `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](O)CNC(=O)c1scnc1Cl) `ZINC001285428311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428311 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 9, 9, 9, 14, 26, 26, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 14, 14, 26, 50] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428311 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 Building ZINC001285428311 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428311 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 269) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428311 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 20, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 20, 20, 28, 50] 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]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 270) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428311 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 9, 9, 9, 14, 26, 26, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 14, 14, 26, 50] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428311 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428311 Building ZINC001285428323 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428323 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/271 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428323 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 9, 9, 9, 14, 26, 26, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 14, 14, 26, 50] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/272 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428323 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 20, 27, 27, 27, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 20, 20, 27, 50] 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]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428323 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 Building ZINC001285428323 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428323 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 271) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428323 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 9, 9, 9, 14, 26, 26, 26, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 27, 14, 14, 26, 50] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 272) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl) `ZINC001285428323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001285428323 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1scnc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 14, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 13, 13, 13, 20, 27, 27, 27, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 39, 20, 20, 27, 50] 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]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428323 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428323 Building ZINC001285428421 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428421 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/273 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 14, 14, 14, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 42, 19, 19, 24, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/274 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 10, 10, 10, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 17, 17, 22, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428421 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 Building ZINC001285428421 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428421 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 273) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 14, 14, 14, 19, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 42, 19, 19, 24, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 274) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 10, 10, 10, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 17, 17, 22, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428421 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428421 Building ZINC001285428422 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428422 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/275 `/scratch/xiaobo/3016/xbk-8058097.37/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@@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 10, 10, 10, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 17, 17, 22, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/276 `/scratch/xiaobo/3016/xbk-8058097.37/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@@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 13, 13, 13, 17, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 17, 17, 24, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428422 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 Building ZINC001285428422 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285428422 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 275) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285428422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 10, 10, 10, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 17, 17, 22, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 276) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](O)CNC(=O)c1cccc2[nH]ccc21) `ZINC001285428422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285428422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285428422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)c1cccc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 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, 13, 13, 13, 17, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 17, 17, 24, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285428422 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285428422 Building ZINC001285475530 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285475530 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/277 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(C)(C)CNC(=O)c1cnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285475530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285475530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285475530 none CN(CC(C)(C)CNC(=O)c1cnn(C)n1)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 16, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 50, 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: 187 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/278 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(C)(C)CNC(=O)c1cnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285475530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285475530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285475530 none CN(CC(C)(C)CNC(=O)c1cnn(C)n1)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 16, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 50, 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: 187 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285475530 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 Building ZINC001285475530 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285475530 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 277) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CC(C)(C)CNC(=O)c1cnn(C)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285475530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285475530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285475530 none CN(CC(C)(C)CNC(=O)c1cnn(C)n1)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 16, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 50, 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: 187 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 278) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(CC(C)(C)CNC(=O)c1cnn(C)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285475530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285475530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285475530 none CN(CC(C)(C)CNC(=O)c1cnn(C)n1)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 16, 16, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 50, 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: 187 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285475530 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285475530 Building ZINC001285504062 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504062 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/279 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285504062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285504062 none COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 48, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/280 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285504062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285504062 none COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 49, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504062 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 Building ZINC001285504062 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504062 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 279) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285504062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285504062 none COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 48, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 280) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285504062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285504062 none COc1nn(C)cc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 49, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504062 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504062 Building ZINC001285504086 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504086 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/281 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/281' -> `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=C/CNC(=O)c1cnn2ccncc12) `ZINC001285504086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504086 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 46, 46, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/282 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/282' -> `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=C/CNC(=O)c1cnn2ccncc12) `ZINC001285504086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504086 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 46, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 46, 46, 49, 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504086 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 Building ZINC001285504086 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504086 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 281) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12) `ZINC001285504086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504086 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 46, 46, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 282) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12) `ZINC001285504086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504086 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cnn2ccncc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 46, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 46, 46, 49, 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504086 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504086 Building ZINC001285504658 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504658 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/283 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285504658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504658 none Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 39, 39, 27, 15, 15, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 27, 27, 15, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/284 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285504658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504658 none Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 39, 39, 28, 15, 15, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 28, 28, 15, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504658 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 Building ZINC001285504658 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504658 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 283) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285504658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504658 none Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 39, 39, 27, 15, 15, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 27, 27, 15, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 284) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001285504658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504658 none Cc1cnn(CCC(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 39, 39, 28, 15, 15, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 28, 28, 15, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504658 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504658 Building ZINC001285504661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/285 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1) `ZINC001285504661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 34, 34, 34, 34, 34, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 34, 34, 34, 34, 50, 50, 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, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/286 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1) `ZINC001285504661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 33, 33, 33, 33, 33, 33, 33, 50, 50, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 33, 33, 33, 33, 50, 50, 33] 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 Building ZINC001285504661 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504661 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 285) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1) `ZINC001285504661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 34, 34, 34, 34, 34, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 34, 34, 34, 34, 50, 50, 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, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 286) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1) `ZINC001285504661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cc(C(N)=O)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 33, 33, 33, 33, 33, 33, 33, 50, 50, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 33, 33, 33, 33, 50, 50, 33] 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504661 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504661 Building ZINC001285504709 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504709 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/287 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1ccc2nn[nH]c2n1) `ZINC001285504709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504709 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1ccc2nn[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.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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, 2, 8, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 42, 42, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/288 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1ccc2nn[nH]c2n1) `ZINC001285504709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504709 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1ccc2nn[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.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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, 2, 8, 24, 24, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 42, 42, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504709 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 Building ZINC001285504709 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504709 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 287) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1ccc2nn[nH]c2n1) `ZINC001285504709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504709 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1ccc2nn[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.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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, 2, 8, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 42, 42, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 288) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1ccc2nn[nH]c2n1) `ZINC001285504709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285504709 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1ccc2nn[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.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 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, 2, 8, 24, 24, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 42, 42, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504709 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504709 Building ZINC001285504726 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504726 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/289 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285504726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285504726 none COc1cnc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 3, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/290 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285504726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285504726 none COc1cnc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 3, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504726 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 Building ZINC001285504726 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504726 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 289) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1cnc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285504726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285504726 none COc1cnc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 3, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 290) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1cnc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285504726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285504726 none COc1cnc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 3, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504726 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504726 Building ZINC001285504729 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504729 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/291 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285504729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504729 none CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 40, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 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, 23, 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/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/292 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285504729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504729 none CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 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, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504729 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 Building ZINC001285504729 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285504729 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 291) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285504729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285504729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504729 none CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total 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, 40, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 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, 23, 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/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 292) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285504729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285504729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285504729 none CN(C)c1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 49, 40, 41, 42, 43, 44, 13, 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, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285504729 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285504729 Building ZINC001285505230 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505230 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/293 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1=O) `ZINC001285505230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285505230 none Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 11, 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, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 44, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [45, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/294 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1=O) `ZINC001285505230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285505230 none Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 11, 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, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 44, 35, 35, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505230 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 Building ZINC001285505230 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505230 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 293) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1=O) `ZINC001285505230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285505230 none Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 11, 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, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 44, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [45, 43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 294) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1=O) `ZINC001285505230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285505230 none Cn1ccc(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 11, 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, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 44, 35, 35, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505230 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505230 Building ZINC001285505250 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505250 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/295 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505250 none CCn1nnc(C)c1C(=O)NC/C=C/CNC(=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 23, 23, 23, 20, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 34, 23, 20, 20, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/296 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505250 none CCn1nnc(C)c1C(=O)NC/C=C/CNC(=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 23, 23, 23, 20, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 34, 23, 20, 20, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505250 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 Building ZINC001285505250 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505250 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 295) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1nnc(C)c1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505250 none CCn1nnc(C)c1C(=O)NC/C=C/CNC(=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 23, 23, 23, 20, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 34, 23, 20, 20, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 296) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1nnc(C)c1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505250 none CCn1nnc(C)c1C(=O)NC/C=C/CNC(=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 23, 23, 23, 20, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 34, 23, 20, 20, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505250 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505250 Building ZINC001285505259 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505259 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/297 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001285505259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285505259 none Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 39, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/298 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001285505259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285505259 none Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 39, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505259 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 Building ZINC001285505259 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505259 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 297) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001285505259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285505259 none Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 39, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 298) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001285505259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285505259 none Cc1cc(=O)c(C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 39, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505259 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505259 Building ZINC001285505456 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505456 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/299 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505456 none C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 43, 36, 36, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/300 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505456 none C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 44, 44, 34, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 34, 34, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505456 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 Building ZINC001285505456 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505456 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 299) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505456 none C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 43, 43, 36, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 43, 36, 36, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 300) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505456 none C[C@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 44, 44, 34, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 34, 34, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505456 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505456 Building ZINC001285505459 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505459 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/301 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505459 none C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 44, 44, 34, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 34, 34, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/302 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505459 none C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 43, 43, 35, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 43, 35, 35, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505459 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 Building ZINC001285505459 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505459 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 301) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505459 none C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 44, 44, 34, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 44, 34, 34, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 302) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285505459 none C[C@@H](Cc1cnc[nH]1)C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 50, 50, 43, 43, 35, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 43, 35, 35, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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/3016/xbk-8058097.37/working/building/ZINC001285505459 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505459 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505459 Building ZINC001285505473 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505473 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/303 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)CC1OCCCO1) `ZINC001285505473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505473 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 40, 40, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/304 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)CC1OCCCO1) `ZINC001285505473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505473 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 39, 39, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505473 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 Building ZINC001285505473 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505473 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 303) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)CC1OCCCO1) `ZINC001285505473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505473 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 40, 40, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 304) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)CC1OCCCO1) `ZINC001285505473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505473 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 27, 39, 39, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505473 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505473 Building ZINC001285505520 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505520 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/305 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505520 none COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 29, 29, 29, 25, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 29, 25, 25, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/306 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505520 none COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 28, 28, 28, 24, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 30, 28, 24, 24, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505520 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 Building ZINC001285505520 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505520 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 305) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285505520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505520 none COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 31, 29, 29, 29, 25, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 29, 25, 25, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 306) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285505520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285505520 none COCc1nocc1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 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, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 28, 28, 28, 24, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 30, 28, 24, 24, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505520 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505520 Building ZINC001285505551 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505551 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/307 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/307' -> `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=C/CNC(=O)c1cncc2nc[nH]c21) `ZINC001285505551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505551 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 20, 30, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 30, 30, 32, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/308 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/308' -> `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=C/CNC(=O)c1cncc2nc[nH]c21) `ZINC001285505551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505551 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 20, 29, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 29, 29, 31, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505551 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 Building ZINC001285505551 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505551 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 307) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[nH]c21) `ZINC001285505551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505551 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 20, 30, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 30, 30, 32, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 308) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[nH]c21) `ZINC001285505551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505551 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cncc2nc[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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 20, 29, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 29, 29, 31, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505551 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505551 Building ZINC001285505819 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505819 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/309 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1) `ZINC001285505819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505819 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 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, 7, 13, 13, 17, 18, 18, 18, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 17, 17, 18, 42, 42, 50, 50, 100, 50] 100 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, 46]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/310 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1) `ZINC001285505819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505819 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 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, 6, 12, 12, 16, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 16, 16, 19, 43, 43, 50, 50, 100, 50] 100 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, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505819 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 Building ZINC001285505819 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285505819 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 309) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1) `ZINC001285505819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285505819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505819 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 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, 7, 13, 13, 17, 18, 18, 18, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 17, 17, 18, 42, 42, 50, 50, 100, 50] 100 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, 46]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 310) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1) `ZINC001285505819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285505819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285505819 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)Cc1ccc(O)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 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, 6, 12, 12, 16, 19, 19, 19, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 16, 16, 19, 43, 43, 50, 50, 100, 50] 100 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, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285505819 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285505819 Building ZINC001285506019 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506019 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/311 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/311' -> `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=C/CNC(=O)c1cn(CC2CC2)nn1) `ZINC001285506019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506019 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 14, 26, 29, 29, 29, 29, 29, 29, 44, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 26, 26, 29, 29, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/312 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/312' -> `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=C/CNC(=O)c1cn(CC2CC2)nn1) `ZINC001285506019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506019 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 14, 26, 29, 29, 29, 29, 29, 29, 43, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 26, 26, 29, 29, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506019 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 Building ZINC001285506019 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506019 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 311) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1) `ZINC001285506019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506019 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 14, 26, 29, 29, 29, 29, 29, 29, 44, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 26, 26, 29, 29, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 312) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1) `ZINC001285506019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506019 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 14, 26, 29, 29, 29, 29, 29, 29, 43, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 26, 26, 29, 29, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506019 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506019 Building ZINC001285506204 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506204 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/313 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/313' -> `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=C/CNC(=O)c1n[nH]c2c1CCC2) `ZINC001285506204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 47, 47, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/314 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/314' -> `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=C/CNC(=O)c1n[nH]c2c1CCC2) `ZINC001285506204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 46, 46, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506204 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 Building ZINC001285506204 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506204 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 313) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2) `ZINC001285506204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 47, 47, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 314) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2) `ZINC001285506204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1n[nH]c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 46, 46, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506204 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506204 Building ZINC001285506214 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506214 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/315 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2) `ZINC001285506214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506214 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 45, 45, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/316 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2) `ZINC001285506214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506214 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 44, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 44, 44, 49, 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506214 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 Building ZINC001285506214 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506214 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 315) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2) `ZINC001285506214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506214 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 45, 45, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 316) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2) `ZINC001285506214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285506214 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC/C=C/CNC(=O)c1nc[nH]c2nccc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 23, 23, 44, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 23, 23, 44, 44, 49, 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506214 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506214 Building ZINC001285506418 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506418 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/317 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285506418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285506418 none C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 50, 39, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/318 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285506418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285506418 none C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 50, 40, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506418 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 Building ZINC001285506418 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285506418 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 317) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285506418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285506418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285506418 none C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 50, 39, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 318) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285506418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285506418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285506418 none C[C@@H]1OCCO[C@@H]1C(=O)NC/C=C/CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 50, 40, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 39, 40, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285506418 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285506418 Building ZINC001285630825 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630825 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/319 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630825 none C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 21, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/320 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630825 none C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 22, 22, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630825 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 Building ZINC001285630825 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630825 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 319) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630825 none C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 21, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 320) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630825 none C[C@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 22, 22, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630825 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630825 Building ZINC001285630826 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630826 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/321 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630826 none C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/322 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630826 none C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630826 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 Building ZINC001285630826 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630826 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 321) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630826 none C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 322) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285630826 none C[C@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630826 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630826 Building ZINC001285630889 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630889 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/323 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285630889 none C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 8, 8, 19, 20, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 19, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/324 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285630889 none C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 8, 8, 8, 19, 21, 39, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 19, 19, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630889 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 Building ZINC001285630889 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285630889 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 323) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285630889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285630889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285630889 none C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 8, 8, 19, 20, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 19, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 324) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285630889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285630889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285630889 none C[C@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 8, 8, 8, 19, 21, 39, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 19, 19, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285630889 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285630889 Building ZINC001285631224 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631224 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/325 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631224 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 14, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/326 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631224 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 26, 26, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631224 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 Building ZINC001285631224 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631224 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 325) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631224 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 14, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 326) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631224 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 26, 26, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631224 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631224 Building ZINC001285631225 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631225 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/327 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631225 none Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 24, 24, 12, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 12, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/328 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631225 none Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 25, 25, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631225 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 Building ZINC001285631225 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631225 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 327) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631225 none Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 24, 24, 12, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 12, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 328) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285631225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631225 none Cc1ncc2n1CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 25, 25, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631225 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631225 Building ZINC001285631512 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631512 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/329 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631512 none C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 43, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/330 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631512 none C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 22, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 45, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631512 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 Building ZINC001285631512 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631512 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 329) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631512 none C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 43, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 330) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631512 none C[C@H](CNC(=O)c1ccc2oc(O)nc2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 22, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 45, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631512 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631512 Building ZINC001285631541 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631541 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/331 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631541 none C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/332 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631541 none C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 36, 36, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631541 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 Building ZINC001285631541 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631541 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 331) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631541 none C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 332) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631541 none C[C@H](CNC(=O)[C@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 36, 36, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631541 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631541 Building ZINC001285631542 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631542 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/333 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631542 none C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 34, 34, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/334 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631542 none C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631542 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 Building ZINC001285631542 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631542 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 333) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631542 none C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 34, 34, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 334) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631542 none C[C@H](CNC(=O)[C@@]1(C)CCCS1(=O)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631542 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631542 Building ZINC001285631557 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631557 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/335 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631557 none C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 25, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/336 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631557 none C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 19, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631557 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 Building ZINC001285631557 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631557 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 335) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631557 none C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 25, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 336) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285631557 none C[C@H](CNC(=O)c1nccn2ccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 19, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631557 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631557 Building ZINC001285631565 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631565 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/337 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285631565 none C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 23, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/338 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285631565 none C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631565 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 Building ZINC001285631565 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631565 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 337) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285631565 none C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 23, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 338) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285631565 none C[C@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631565 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631565 Building ZINC001285631591 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631591 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/339 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285631591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631591 none COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 27, 27, 27, 26, 26, 26, 16, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 45, 45, 27, 27, 26, 16, 16, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/340 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285631591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631591 none COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 32, 32, 32, 32, 32, 32, 14, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 46, 46, 32, 32, 32, 14, 14, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631591 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 Building ZINC001285631591 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631591 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 339) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285631591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631591 none COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 27, 27, 27, 26, 26, 26, 16, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 45, 45, 27, 27, 26, 16, 16, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 340) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285631591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631591 none COCCn1ccc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 32, 32, 32, 32, 32, 32, 14, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 46, 46, 32, 32, 32, 14, 14, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631591 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631591 Building ZINC001285631614 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631614 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/341 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631614 none C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 13, 13, 13, 38, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/342 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631614 none C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 10, 10, 10, 31, 38, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631614 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 Building ZINC001285631614 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631614 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 341) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631614 none C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 13, 13, 13, 38, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 342) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631614 none C[C@H](CNC(=O)CC[C@@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 10, 10, 10, 31, 38, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631614 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631614 Building ZINC001285631615 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631615 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/343 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631615 none C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 13, 13, 13, 36, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 13, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/344 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631615 none C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 5, 9, 9, 9, 33, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631615 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 Building ZINC001285631615 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631615 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 343) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631615 none C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 13, 13, 13, 36, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 13, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 344) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631615 none C[C@H](CNC(=O)CC[C@]1(C)CCC(=O)N1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 5, 9, 9, 9, 33, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631615 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631615 Building ZINC001285631675 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631675 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/345 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631675 none Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 26, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 42, 26, 26, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/346 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631675 none Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 27, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 43, 27, 27, 10, 10, 10, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631675 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 Building ZINC001285631675 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631675 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 345) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631675 none Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 26, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 42, 26, 26, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 346) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631675 none Cc1ccn2ncc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 27, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 43, 27, 27, 10, 10, 10, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631675 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631675 Building ZINC001285631707 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631707 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/347 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631707 none Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 11, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 14, 11, 11, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/348 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631707 none Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 14, 10, 10, 4, 4, 4, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631707 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 Building ZINC001285631707 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631707 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 347) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631707 none Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 11, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 14, 11, 11, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 348) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1) `ZINC001285631707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285631707 none Cc1cn2ccnc(C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 14, 10, 10, 4, 4, 4, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631707 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631707 Building ZINC001285631776 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631776 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/349 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631776 none C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 31, 31, 31, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 31, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/350 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631776 none C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 34, 34, 34, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 34, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631776 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 Building ZINC001285631776 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631776 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 349) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631776 none C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 31, 31, 31, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 31, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 350) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631776 none C[C@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 34, 34, 34, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 34, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631776 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631776 Building ZINC001285631796 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631796 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/351 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631796 none COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 28, 28, 18, 18, 18, 10, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 28, 18, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/352 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631796 none COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 17, 17, 17, 10, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 27, 17, 10, 10, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631796 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 Building ZINC001285631796 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631796 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 351) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631796 none COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 28, 28, 18, 18, 18, 10, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 28, 18, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 352) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285631796 none COCc1nocc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 17, 17, 17, 10, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 27, 17, 10, 10, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631796 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631796 Building ZINC001285631800 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631800 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/353 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631800 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 23, 43, 23, 23, 17, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 17, 17, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/354 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631800 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 39, 20, 20, 16, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 16, 16, 12, 12, 12, 4, 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: 150 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631800 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 Building ZINC001285631800 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631800 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 353) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631800 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 23, 43, 23, 23, 17, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 17, 17, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 354) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631800 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 20, 39, 20, 20, 16, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 16, 16, 12, 12, 12, 4, 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: 150 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631800 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631800 Building ZINC001285631801 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631801 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/355 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631801 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 42, 21, 42, 21, 21, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 21, 16, 16, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/356 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631801 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 23, 45, 23, 23, 18, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 23, 18, 18, 12, 12, 12, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631801 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 Building ZINC001285631801 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631801 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 355) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631801 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 42, 21, 42, 21, 21, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 21, 16, 16, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 356) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631801 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 23, 45, 23, 23, 18, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 23, 18, 18, 12, 12, 12, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631801 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631801 Building ZINC001285631810 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631810 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/357 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631810 none C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 11, 18, 18, 18, 37, 39, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 18, 37, 37, 39, 39, 50, 50, 100, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/358 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631810 none C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 18, 18, 18, 44, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 18, 44, 44, 45, 45, 50, 50, 100, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631810 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 Building ZINC001285631810 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631810 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 357) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631810 none C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 11, 18, 18, 18, 37, 39, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 18, 37, 37, 39, 39, 50, 50, 100, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 358) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631810 none C[C@H](CNC(=O)CCc1ccc(O)nc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 10, 18, 18, 18, 44, 45, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 18, 44, 44, 45, 45, 50, 50, 100, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631810 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631810 Building ZINC001285631811 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631811 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/359 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631811 none C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 21, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/360 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631811 none C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 20, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 40, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631811 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 Building ZINC001285631811 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631811 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 359) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631811 none C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 21, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 360) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631811 none C[C@H](CNC(=O)c1cn2c(n1)COCC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 20, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 40, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631811 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631811 Building ZINC001285631819 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631819 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/361 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631819 none C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 25, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/362 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631819 none C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 20, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631819 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 Building ZINC001285631819 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631819 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 361) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631819 none C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 25, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 362) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285631819 none C[C@H](CNC(=O)c1cc(N(C)C)ccn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 20, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631819 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631819 Building ZINC001285631840 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631840 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/363 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631840 none C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 17, 31, 31, 31, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 31, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/364 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631840 none C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 18, 31, 31, 31, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 31, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631840 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 Building ZINC001285631840 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631840 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 363) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631840 none C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 17, 31, 31, 31, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 31, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 364) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631840 none C[C@H](CNC(=O)[C@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 18, 31, 31, 31, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 31, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631840 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631840 Building ZINC001285631841 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631841 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/365 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631841 none C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/366 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631841 none C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 30, 30, 30, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 30, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631841 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 Building ZINC001285631841 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631841 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 365) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631841 none C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 19, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 36, 36, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 366) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285631841 none C[C@H](CNC(=O)[C@@H](c1cccnc1)N(C)C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 8, 1, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 30, 30, 30, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 30, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 44, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631841 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631841 Building ZINC001285631930 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631930 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/367 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631930 none C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 16, 16, 16, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 16, 39, 39, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/368 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631930 none C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 15, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 15, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631930 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 Building ZINC001285631930 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285631930 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 367) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285631930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285631930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631930 none C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 16, 16, 16, 39, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 16, 39, 39, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 368) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285631930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285631930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285631930 none C[C@H](CNC(=O)Cc1ccccc1C(N)=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 15, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 15, 37, 37, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285631930 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285631930 Building ZINC001285632018 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632018 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/369 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632018 none CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 34, 42, 34, 34, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 34, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/370 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632018 none CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 36, 36, 19, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 36, 19, 19, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632018 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 Building ZINC001285632018 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632018 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 369) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632018 none CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 34, 42, 34, 34, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 34, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 370) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632018 none CC[C@@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 36, 36, 19, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 36, 19, 19, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632018 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632018 Building ZINC001285632019 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632019 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/371 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632019 none CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 43, 46, 43, 43, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 43, 19, 19, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/372 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632019 none CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 44, 47, 44, 44, 22, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 44, 22, 22, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632019 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 Building ZINC001285632019 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632019 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 371) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632019 none CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 43, 46, 43, 43, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 43, 19, 19, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 372) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O) `ZINC001285632019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285632019 none CC[C@H](C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 44, 47, 44, 44, 22, 10, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 44, 22, 22, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632019 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632019 Building ZINC001285632188 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632188 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/373 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632188 none C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/374 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632188 none C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 26, 26, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 26, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632188 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 Building ZINC001285632188 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632188 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 373) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632188 none C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 374) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632188 none C[C@H](CNC(=O)[C@@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 26, 26, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 26, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632188 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632188 Building ZINC001285632189 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632189 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/375 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632189 none C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 21, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/376 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632189 none C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 21, 21, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 21, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632189 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 Building ZINC001285632189 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632189 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 375) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632189 none C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 21, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 376) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285632189 none C[C@H](CNC(=O)[C@H]1CCc2c[nH]nc2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 21, 21, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 21, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 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]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632189 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632189 Building ZINC001285632221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/377 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285632221 none C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 12, 20, 20, 20, 46, 46, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 20, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 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: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/378 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285632221 none C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 18, 18, 18, 47, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 18, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 Building ZINC001285632221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 377) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285632221 none C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 12, 20, 20, 20, 46, 46, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 20, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 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: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 378) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285632221 none C[C@H](CNC(=O)CCN1CCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 18, 18, 18, 47, 47, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 18, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632221 Building ZINC001285632241 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632241 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/379 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632241 none Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 20, 20, 20, 13, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 13, 13, 6, 6, 6, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/380 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632241 none Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 23, 23, 23, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 23, 16, 16, 7, 7, 7, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632241 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 Building ZINC001285632241 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632241 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 379) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632241 none Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 20, 20, 20, 13, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 13, 13, 6, 6, 6, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 380) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632241 none Cc1nn(C)c(C)c1CC(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 23, 23, 23, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 23, 16, 16, 7, 7, 7, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632241 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632241 Building ZINC001285632274 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632274 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/381 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632274 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/382 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632274 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 18, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632274 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 Building ZINC001285632274 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632274 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 381) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632274 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 382) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632274 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 18, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632274 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632274 Building ZINC001285632275 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632275 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/383 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632275 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/384 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632275 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 16, 31, 31, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632275 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 Building ZINC001285632275 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285632275 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 383) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285632275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285632275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632275 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 384) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285632275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285632275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285632275 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 16, 31, 31, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285632275 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285632275 Building ZINC001285633074 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633074 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/385 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633074 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 38, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/386 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633074 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 40, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633074 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 Building ZINC001285633074 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633074 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 385) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633074 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 38, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 386) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633074 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 40, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633074 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633074 Building ZINC001285633078 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633078 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/387 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633078 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 42, 42, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/388 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633078 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633078 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 Building ZINC001285633078 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633078 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 387) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633078 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 42, 42, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 388) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12) `ZINC001285633078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633078 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1C[C@@H]2O[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 5, 38, 7, 8, 9, 10, 11, 12, 44, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633078 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633078 Building ZINC001285633105 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633105 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/389 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285633105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633105 none Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 26, 18, 26, 18, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 18, 18, 18, 18, 18, 10, 10, 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: 197 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/390 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285633105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633105 none Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 19, 30, 17, 19, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 17, 17, 17, 9, 9, 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: 185 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633105 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 Building ZINC001285633105 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633105 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 389) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285633105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633105 none Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 26, 18, 26, 18, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 18, 18, 18, 18, 18, 10, 10, 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: 197 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 390) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285633105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633105 none Cc1nn(C)cc1CC(=O)N(C)[C@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 19, 30, 17, 19, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 17, 17, 17, 9, 9, 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: 185 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633105 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633105 Building ZINC001285633108 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633108 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/391 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285633108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633108 none Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 19, 30, 17, 19, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 17, 17, 17, 9, 9, 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: 185 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/392 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285633108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633108 none Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 24, 18, 24, 18, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 18, 18, 18, 18, 18, 10, 10, 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: 204 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633108 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 Building ZINC001285633108 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633108 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 391) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285633108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633108 none Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 19, 30, 17, 19, 9, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 19, 19, 19, 17, 17, 17, 9, 9, 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: 185 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 392) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285633108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285633108 none Cc1nn(C)cc1CC(=O)N(C)[C@@H](C)CNC(=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.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 24, 18, 24, 18, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 18, 18, 18, 18, 18, 18, 10, 10, 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: 204 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633108 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633108 Building ZINC001285633283 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633283 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/393 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633283 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 34, 34, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/394 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633283 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633283 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 Building ZINC001285633283 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633283 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 393) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633283 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 34, 34, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 394) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633283 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633283 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633283 Building ZINC001285633284 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633284 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/395 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633284 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/396 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633284 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633284 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 Building ZINC001285633284 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633284 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 395) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633284 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 396) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21) `ZINC001285633284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285633284 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccnc2[nH]nnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633284 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633284 Building ZINC001285633313 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633313 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/397 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633313 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 31, 31, 37, 37, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 37, 37, 37, 37, 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: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/398 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633313 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 32, 32, 33, 33, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 33, 33, 33, 33, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633313 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 Building ZINC001285633313 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633313 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 397) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633313 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 31, 31, 37, 37, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 37, 37, 37, 37, 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: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 398) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633313 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 32, 32, 33, 33, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 33, 33, 33, 33, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633313 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633313 Building ZINC001285633314 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633314 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/399 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633314 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 29, 29, 33, 33, 34, 34, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 34, 34, 34, 34, 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/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/400 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633314 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 30, 30, 36, 36, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 36, 36, 36, 36, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633314 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 Building ZINC001285633314 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633314 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 399) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633314 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 29, 29, 33, 33, 34, 34, 50, 50, 50, 50, 50, 19, 19, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 34, 34, 34, 34, 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/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 400) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1) `ZINC001285633314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285633314 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCc1cnn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 25, 25, 30, 30, 36, 36, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 36, 36, 36, 36, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633314 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633314 Building ZINC001285633623 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633623 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/401 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633623 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 17, 17, 20, 20, 21, 21, 21, 41, 50, 50, 21, 21, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 21, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/402 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633623 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 24, 24, 24, 24, 24, 46, 50, 50, 24, 24, 14, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 24, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633623 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 Building ZINC001285633623 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633623 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 401) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633623 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 17, 17, 20, 20, 21, 21, 21, 41, 50, 50, 21, 21, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 21, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 402) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633623 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 24, 24, 24, 24, 24, 46, 50, 50, 24, 24, 14, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 24, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633623 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633623 Building ZINC001285633624 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633624 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/403 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633624 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 16, 16, 21, 21, 21, 21, 21, 44, 50, 50, 21, 21, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 21, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/404 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633624 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 19, 19, 20, 20, 20, 41, 50, 50, 20, 20, 15, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 20, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633624 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 Building ZINC001285633624 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633624 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 403) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633624 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 16, 16, 21, 21, 21, 21, 21, 44, 50, 50, 21, 21, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 21, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 404) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1) `ZINC001285633624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285633624 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 19, 19, 20, 20, 20, 41, 50, 50, 20, 20, 15, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 20, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633624 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633624 Building ZINC001285633633 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633633 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/405 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633633 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 33, 33, 40, 40, 48, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/406 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633633 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633633 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 Building ZINC001285633633 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633633 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 405) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633633 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 33, 33, 40, 40, 48, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 406) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633633 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633633 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633633 Building ZINC001285633634 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633634 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/407 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633634 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/408 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633634 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 33, 33, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633634 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 Building ZINC001285633634 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633634 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 407) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633634 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 32, 32, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 408) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633634 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 33, 33, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633634 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633634 Building ZINC001285633635 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633635 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/409 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633635 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 28, 28, 33, 33, 44, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/410 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633635 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 35, 35, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633635 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 Building ZINC001285633635 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633635 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 409) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633635 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 28, 28, 33, 33, 44, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 410) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C) `ZINC001285633635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633635 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 28, 28, 35, 35, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633635 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633635 Building ZINC001285633636 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633636 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/411 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633636 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 28, 28, 35, 35, 49, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/412 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633636 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 28, 28, 33, 33, 44, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633636 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 Building ZINC001285633636 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633636 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 411) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633636 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 28, 28, 35, 35, 49, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 412) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C) `ZINC001285633636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633636 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 28, 28, 33, 33, 44, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633636 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633636 Building ZINC001285633665 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633665 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/413 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633665 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/414 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633665 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633665 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 Building ZINC001285633665 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633665 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 413) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633665 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 414) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633665 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 36, 36, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633665 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633665 Building ZINC001285633666 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633666 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/415 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633666 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 35, 35, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/416 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633666 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 41, 41, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633666 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 Building ZINC001285633666 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633666 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 415) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633666 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 35, 35, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 416) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633666 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 41, 41, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633666 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633666 Building ZINC001285633667 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633667 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/417 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633667 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/418 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633667 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 36, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633667 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 Building ZINC001285633667 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633667 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 417) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633667 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 418) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C) `ZINC001285633667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633667 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 36, 35, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633667 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633667 Building ZINC001285633668 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633668 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/419 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633668 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 36, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/420 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633668 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 205 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633668 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 Building ZINC001285633668 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633668 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 419) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633668 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 36, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 420) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C) `ZINC001285633668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285633668 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 205 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633668 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633668 Building ZINC001285633683 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633683 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/421 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633683 none CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 20, 20, 20, 19, 20, 10, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 28, 28, 20, 20, 20, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/422 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633683 none CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 24, 24, 24, 21, 24, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 40, 33, 33, 24, 24, 24, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633683 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 Building ZINC001285633683 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633683 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 421) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633683 none CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 20, 20, 20, 19, 20, 10, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 28, 28, 20, 20, 20, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 422) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633683 none CCn1cc(CC(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 24, 24, 24, 21, 24, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 40, 33, 33, 24, 24, 24, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633683 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633683 Building ZINC001285633684 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633684 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/423 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633684 none CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 23, 23, 23, 21, 23, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 40, 33, 33, 23, 23, 23, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/424 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633684 none CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 20, 20, 20, 19, 20, 10, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 28, 28, 20, 20, 20, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633684 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 Building ZINC001285633684 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285633684 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 423) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285633684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633684 none CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 23, 23, 23, 21, 23, 10, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 40, 33, 33, 23, 23, 23, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 424) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001285633684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285633684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285633684 none CCn1cc(CC(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 20, 20, 20, 19, 20, 10, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 50, 50, 50, 50, 50, 37, 28, 28, 20, 20, 20, 19, 19, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285633684 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285633684 Building ZINC001285634122 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634122 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/425 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634122 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/426 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634122 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634122 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 Building ZINC001285634122 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634122 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 425) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634122 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 426) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634122 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634122 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634122 Building ZINC001285634123 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634123 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/427 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634123 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/428 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634123 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634123 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 Building ZINC001285634123 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634123 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 427) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634123 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 35, 35, 44, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 428) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634123 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 31, 31, 43, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634123 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634123 Building ZINC001285634124 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634124 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/429 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634124 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 31, 31, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/430 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634124 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 24, 23, 30, 31, 44, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634124 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 Building ZINC001285634124 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634124 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 429) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634124 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 31, 31, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 430) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1) `ZINC001285634124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634124 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 24, 23, 30, 31, 44, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634124 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634124 Building ZINC001285634125 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634125 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/431 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634125 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 24, 23, 30, 31, 44, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/432 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634125 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 25, 30, 30, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 34, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634125 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 Building ZINC001285634125 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634125 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 431) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634125 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 24, 23, 30, 31, 44, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 432) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1) `ZINC001285634125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285634125 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)C[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 25, 30, 30, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 34, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634125 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634125 Building ZINC001285634449 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634449 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/433 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634449 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 45, 45, 45, 45, 45, 45, 50, 50, 45, 45, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 45, 45, 50, 50, 45, 45] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/434 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634449 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 34, 34, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 43, 43, 50, 50, 43, 43] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634449 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 Building ZINC001285634449 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634449 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 433) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634449 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 45, 45, 45, 45, 45, 45, 50, 50, 45, 45, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 45, 45, 50, 50, 45, 45] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 434) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634449 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 34, 34, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 43, 43, 50, 50, 43, 43] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634449 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634449 Building ZINC001285634450 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634450 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/435 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634450 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 34, 34, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 43, 43, 50, 50, 43, 43] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/436 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634450 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 44, 44, 44, 44, 44, 44, 50, 50, 44, 44, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 44, 44, 50, 50, 44, 44] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634450 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 Building ZINC001285634450 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634450 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 435) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634450 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 34, 34, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 43, 43, 50, 50, 43, 43] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 436) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1) `ZINC001285634450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634450 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 44, 44, 44, 44, 44, 44, 50, 50, 44, 44, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 44, 44, 50, 50, 44, 44] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634450 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634450 Building ZINC001285634837 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634837 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/437 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634837 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 25, 25, 30, 43, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/438 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634837 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 26, 26, 35, 44, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634837 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 Building ZINC001285634837 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634837 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 437) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634837 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 25, 25, 30, 43, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 438) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634837 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 26, 26, 35, 44, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634837 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634837 Building ZINC001285634838 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634838 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/439 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634838 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 26, 26, 35, 44, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/440 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634838 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 24, 24, 29, 44, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634838 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 Building ZINC001285634838 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285634838 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 439) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285634838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634838 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 26, 26, 35, 44, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 440) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1) `ZINC001285634838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285634838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285634838 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)COc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 20, 20, 24, 24, 29, 44, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285634838 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285634838 Building ZINC001285635737 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285635737 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/441 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285635737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635737 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 42, 41, 47, 49, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/442 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285635737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635737 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 47, 47, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285635737 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 Building ZINC001285635737 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285635737 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 441) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285635737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635737 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 42, 41, 47, 49, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 442) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285635737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635737 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 47, 47, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285635737 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635737 Building ZINC001285635738 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285635738 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/443 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285635738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635738 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 48, 48, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/444 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285635738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635738 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 49, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285635738 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 Building ZINC001285635738 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285635738 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 443) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285635738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635738 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 48, 48, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 444) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C) `ZINC001285635738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285635738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285635738 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)[C@H]1CCC(=O)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 7, 5, 5, 1, 11, 8, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 42, 42, 49, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285635738 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285635738 Building ZINC001285636075 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636075 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/445 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636075 none CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 29, 35, 12, 29, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/446 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636075 none CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 48, 35, 48, 27, 35, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 49, 50, 50, 50, 50, 35, 35, 35, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636075 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 Building ZINC001285636075 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636075 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 445) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636075 none CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 50, 29, 35, 12, 29, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 446) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636075 none CNC(=O)C1(C(=O)N(C)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 48, 35, 48, 27, 35, 11, 27, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 49, 50, 50, 50, 50, 35, 35, 35, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636075 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636075 Building ZINC001285636076 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636076 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/447 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636076 none CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 34, 46, 25, 34, 12, 25, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/448 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636076 none CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 28, 36, 14, 28, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 28, 28, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636076 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 Building ZINC001285636076 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636076 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 447) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636076 none CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 34, 46, 25, 34, 12, 25, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 448) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285636076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285636076 none CNC(=O)C1(C(=O)N(C)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 28, 36, 14, 28, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 28, 28, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636076 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636076 Building ZINC001285636101 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636101 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/449 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1) `ZINC001285636101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285636101 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 26, 26, 29, 29, 34, 34, 50, 50, 50, 50, 50, 15, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/450 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1) `ZINC001285636101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285636101 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 29, 29, 35, 35, 37, 37, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636101 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 Building ZINC001285636101 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636101 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 449) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1) `ZINC001285636101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285636101 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 26, 26, 29, 29, 34, 34, 50, 50, 50, 50, 50, 15, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 450) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1) `ZINC001285636101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285636101 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 29, 29, 35, 35, 37, 37, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/3016/xbk-8058097.37/working/building/ZINC001285636101 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636101 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636101 Building ZINC001285636135 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636135 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/451 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636135 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 41, 45, 46, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 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]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/452 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636135 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 37, 43, 43, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636135 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 Building ZINC001285636135 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636135 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 451) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636135 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 41, 45, 46, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 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]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 452) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636135 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 37, 43, 43, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636135 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636135 Building ZINC001285636136 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636136 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/453 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636136 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 43, 43, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/454 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636136 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 46, 46, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636136 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 Building ZINC001285636136 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636136 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 453) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636136 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 43, 43, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 454) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1) `ZINC001285636136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285636136 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1ccn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 46, 46, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636136 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636136 Building ZINC001285636163 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636163 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/455 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636163 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/456 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636163 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636163 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 Building ZINC001285636163 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636163 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 455) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636163 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 456) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636163 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636163 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636163 Building ZINC001285636164 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636164 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/457 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636164 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/458 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636164 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636164 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 Building ZINC001285636164 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285636164 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 457) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285636164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636164 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 458) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1) `ZINC001285636164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285636164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285636164 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N(C)C(=O)c1cn2cccnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 8, 1, 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, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285636164 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285636164 Building ZINC001285649375 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285649375 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/459 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285649375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285649375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285649375 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/460 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285649375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285649375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285649375 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285649375 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 Building ZINC001285649375 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285649375 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 459) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285649375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285649375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285649375 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 460) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285649375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285649375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285649375 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285649375 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285649375 Building ZINC001285650885 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285650885 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/461 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl) `ZINC001285650885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285650885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285650885 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/462 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl) `ZINC001285650885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285650885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285650885 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 30, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285650885 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 Building ZINC001285650885 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285650885 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 461) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl) `ZINC001285650885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285650885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285650885 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 34, 34, 34, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 462) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl) `ZINC001285650885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285650885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001285650885 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nn(C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 30, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285650885 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285650885 Building ZINC001285653774 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285653774 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/463 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001285653774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285653774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285653774 none Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 21, 16, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 21, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 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, 50, 51]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/464 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001285653774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285653774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285653774 none Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 13, 13, 13, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 41, 37, 37, 13, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 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, 50, 51]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285653774 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 Building ZINC001285653774 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285653774 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 463) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001285653774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285653774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285653774 none Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 21, 16, 8, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 21, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 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, 50, 51]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 464) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001285653774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285653774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285653774 none Cc1c(CCC(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 13, 13, 13, 11, 6, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 41, 37, 37, 13, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 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, 50, 51]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285653774 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285653774 Building ZINC001285654426 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285654426 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/465 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2) `ZINC001285654426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285654426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285654426 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/466 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2) `ZINC001285654426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285654426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285654426 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285654426 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 Building ZINC001285654426 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285654426 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 465) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2) `ZINC001285654426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285654426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285654426 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 466) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2) `ZINC001285654426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285654426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285654426 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1noc2c1COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285654426 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285654426 Building ZINC001285657933 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285657933 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/467 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001285657933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285657933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285657933 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 32, 42, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/468 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001285657933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285657933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285657933 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 19, 25, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 25, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285657933 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 Building ZINC001285657933 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285657933 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 467) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001285657933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285657933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285657933 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 32, 42, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 468) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001285657933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285657933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285657933 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 19, 25, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 25, 25, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285657933 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285657933 Building ZINC001285663192 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663192 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/469 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285663192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285663192 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/470 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285663192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285663192 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663192 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 Building ZINC001285663192 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663192 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 469) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285663192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285663192 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 470) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285663192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285663192 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663192 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663192 Building ZINC001285663527 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663527 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/471 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1) `ZINC001285663527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663527 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/472 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1) `ZINC001285663527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663527 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663527 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 Building ZINC001285663527 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663527 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 471) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1) `ZINC001285663527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663527 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 472) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1) `ZINC001285663527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663527 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663527 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663527 Building ZINC001285663528 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663528 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/473 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1) `ZINC001285663528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663528 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/474 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1) `ZINC001285663528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663528 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663528 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 Building ZINC001285663528 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285663528 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 473) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1) `ZINC001285663528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285663528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663528 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 474) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1) `ZINC001285663528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285663528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285663528 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2nccn2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285663528 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285663528 Building ZINC001285666525 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285666525 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/475 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285666525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285666525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285666525 none CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 34, 34, 23, 11, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 50, 50, 50, 50, 34, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48] 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, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/476 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285666525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285666525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285666525 none CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 17, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 50, 50, 50, 50, 31, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47] 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, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285666525 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 Building ZINC001285666525 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285666525 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 475) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285666525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285666525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285666525 none CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 34, 34, 23, 11, 23, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 50, 50, 50, 50, 34, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48] 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, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 476) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285666525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285666525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285666525 none CC(=O)NC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 31, 31, 31, 17, 10, 17, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 50, 50, 50, 50, 31, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47] 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, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285666525 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285666525 Building ZINC001285667428 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285667428 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/477 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1) `ZINC001285667428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285667428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285667428 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 42, 42, 42, 46, 46, 46, 50, 50, 46, 46, 46, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 46, 50, 50, 46, 46] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/478 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1) `ZINC001285667428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285667428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285667428 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 40, 40, 47, 47, 47, 50, 50, 47, 47, 47, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 47, 50, 50, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285667428 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 Building ZINC001285667428 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285667428 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 477) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1) `ZINC001285667428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285667428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285667428 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 42, 42, 42, 46, 46, 46, 50, 50, 46, 46, 46, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 46, 50, 50, 46, 46] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 478) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1) `ZINC001285667428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285667428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285667428 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 40, 40, 47, 47, 47, 50, 50, 47, 47, 47, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 47, 50, 50, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285667428 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285667428 Building ZINC001285668368 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668368 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/479 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285668368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668368 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/480 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285668368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668368 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668368 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 Building ZINC001285668368 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668368 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 479) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285668368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668368 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 480) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285668368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668368 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668368 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668368 Building ZINC001285668369 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668369 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/481 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285668369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668369 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/482 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285668369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668369 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 45, 45, 45, 45, 45, 45, 50, 50, 45, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 45, 45, 45, 45, 45, 45, 50, 50, 45, 45] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668369 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 Building ZINC001285668369 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668369 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 481) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285668369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668369 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 482) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285668369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285668369 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 45, 45, 45, 45, 45, 45, 50, 50, 45, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 45, 45, 45, 45, 45, 45, 50, 50, 45, 45] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668369 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668369 Building ZINC001285668906 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668906 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/483 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O) `ZINC001285668906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285668906 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 49, 50, 50, 50, 50, 50, 50, 23, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/484 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O) `ZINC001285668906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285668906 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 48, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668906 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 Building ZINC001285668906 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285668906 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 483) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O) `ZINC001285668906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285668906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285668906 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 49, 50, 50, 50, 50, 50, 50, 23, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 484) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O) `ZINC001285668906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285668906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285668906 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 48, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285668906 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285668906 Building ZINC001285672219 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285672219 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/485 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[nH]1) `ZINC001285672219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285672219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285672219 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 32, 35, 39, 47, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 39, 39, 37, 39, 47, 47, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/486 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[nH]1) `ZINC001285672219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285672219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285672219 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 23, 25, 32, 38, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 29, 29, 32, 32, 39, 39, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285672219 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 Building ZINC001285672219 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285672219 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 485) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[nH]1) `ZINC001285672219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285672219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285672219 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 32, 35, 39, 47, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 39, 39, 37, 39, 47, 47, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 486) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[nH]1) `ZINC001285672219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285672219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285672219 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCCc1cnn[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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 23, 25, 32, 38, 50, 50, 50, 50, 50, 8, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 29, 29, 32, 32, 39, 39, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285672219 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285672219 Building ZINC001285678907 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285678907 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/487 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O) `ZINC001285678907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285678907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285678907 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 39, 27, 44, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 39, 39, 39, 39, 40, 42, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/488 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O) `ZINC001285678907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285678907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285678907 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 33, 22, 39, 50, 50, 50, 50, 50, 50, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 34, 34, 39, 34, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285678907 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 Building ZINC001285678907 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285678907 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 487) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O) `ZINC001285678907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285678907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285678907 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 39, 27, 44, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 39, 39, 39, 39, 40, 42, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 488) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O) `ZINC001285678907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285678907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285678907 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 33, 22, 39, 50, 50, 50, 50, 50, 50, 12, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 34, 34, 39, 34, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285678907 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285678907 Building ZINC001285681677 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285681677 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/489 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285681677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285681677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681677 none C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 28, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 49, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/490 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285681677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285681677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681677 none C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285681677 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 Building ZINC001285681677 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285681677 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 489) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285681677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285681677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681677 none C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 28, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 49, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 490) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285681677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285681677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681677 none C[C@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285681677 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681677 Building ZINC001285681679 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285681679 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/491 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285681679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285681679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681679 none C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 49, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/492 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285681679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285681679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681679 none C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285681679 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 Building ZINC001285681679 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285681679 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 491) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285681679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285681679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681679 none C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 25, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 49, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 492) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285681679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285681679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285681679 none C[C@@H](CNC(=O)c1cnc2cccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285681679 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285681679 Building ZINC001285682644 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285682644 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/493 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001285682644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285682644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285682644 none CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 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, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 23, 23, 23, 18, 7, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 23, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/494 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001285682644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285682644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285682644 none CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 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, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need 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, 21, 21, 21, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 50, 50, 50, 50, 50, 21, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 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: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285682644 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 Building ZINC001285682644 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285682644 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 493) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001285682644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285682644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285682644 none CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 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, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 23, 23, 23, 18, 7, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 23, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 494) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O) `ZINC001285682644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285682644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285682644 none CCn1nc(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 11, 7, 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, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need 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, 21, 21, 21, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 50, 50, 50, 50, 50, 21, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 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: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285682644 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285682644 Building ZINC001285694580 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285694580 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/495 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1) `ZINC001285694580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285694580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285694580 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 46, 46, 50, 46, 50, 50, 46, 50, 50, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 46, 46, 50, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/496 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1) `ZINC001285694580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285694580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285694580 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 26, 44, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285694580 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 Building ZINC001285694580 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285694580 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 495) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1) `ZINC001285694580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285694580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285694580 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 31, 31, 46, 46, 50, 46, 50, 50, 46, 50, 50, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 46, 46, 50, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 496) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1) `ZINC001285694580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285694580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285694580 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 26, 26, 26, 44, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285694580 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285694580 Building ZINC001285697375 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285697375 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/497 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2) `ZINC001285697375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285697375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285697375 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/498 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2) `ZINC001285697375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285697375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285697375 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 17, 35, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285697375 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 Building ZINC001285697375 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285697375 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 497) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2) `ZINC001285697375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285697375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285697375 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 39, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 498) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2) `ZINC001285697375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285697375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285697375 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1nnc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 17, 35, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285697375 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285697375 Building ZINC001285707963 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285707963 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/499 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285707963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285707963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707963 none C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 14, 14, 14, 39, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 14, 39, 39, 47, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/500 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285707963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285707963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707963 none C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 15, 15, 15, 38, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 38, 38, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 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/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285707963 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 Building ZINC001285707963 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285707963 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 499) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285707963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285707963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707963 none C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 14, 14, 14, 39, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 14, 39, 39, 47, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 500) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285707963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285707963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707963 none C[C@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 15, 15, 15, 38, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 38, 38, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 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/3016/xbk-8058097.37/working/building/ZINC001285707963 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285707963 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707963 Building ZINC001285707965 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285707965 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/501 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285707965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285707965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707965 none C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 9, 17, 17, 17, 38, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 17, 38, 38, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/502 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285707965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285707965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707965 none C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 13, 13, 13, 38, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 38, 38, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285707965 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 Building ZINC001285707965 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285707965 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 501) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285707965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285707965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707965 none C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 9, 17, 17, 17, 38, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 17, 38, 38, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 502) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285707965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285707965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285707965 none C[C@@H](CNC(=O)CCc1ccn(C)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 13, 13, 13, 38, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 38, 38, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285707965 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285707965 Building ZINC001285708297 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708297 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/503 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708297 none Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 14, 6, 2, 6, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 20, 14, 14, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/504 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708297 none Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 19, 19, 19, 10, 5, 2, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 19, 10, 10, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708297 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 Building ZINC001285708297 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708297 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 503) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708297 none Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 14, 6, 2, 6, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 20, 14, 14, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 504) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708297 none Cc1cc(OCC(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 19, 19, 19, 10, 5, 2, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 19, 10, 10, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708297 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708297 Building ZINC001285708298 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708298 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/505 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708298 none Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 12, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 21, 12, 12, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/506 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708298 none Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 14, 6, 2, 6, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 20, 14, 14, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708298 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 Building ZINC001285708298 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708298 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 505) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708298 none Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 12, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 21, 12, 12, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 506) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1) `ZINC001285708298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285708298 none Cc1cc(OCC(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 14, 6, 2, 6, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 20, 14, 14, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708298 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708298 Building ZINC001285708979 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708979 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/507 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285708979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708979 none C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 22, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 43, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/508 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285708979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708979 none C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708979 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 Building ZINC001285708979 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708979 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 507) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285708979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708979 none C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 22, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 43, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 508) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285708979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708979 none C[C@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708979 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708979 Building ZINC001285708980 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708980 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/509 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285708980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708980 none C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/510 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285708980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708980 none C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 21, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 43, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708980 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 Building ZINC001285708980 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285708980 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 509) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285708980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285708980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708980 none C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 510) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285708980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285708980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285708980 none C[C@@H](CNC(=O)c1ccnc2ccnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 21, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 43, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285708980 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285708980 Building ZINC001285709279 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709279 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/511 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709279 none C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 3, 5, 5, 9, 20, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 20, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/512 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709279 none C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 13, 25, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709279 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 Building ZINC001285709279 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709279 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 511) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709279 none C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 3, 5, 5, 9, 20, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 20, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 512) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709279 none C[C@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 13, 25, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709279 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709279 Building ZINC001285709280 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709280 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/513 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709280 none C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 22, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 22, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/514 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709280 none C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 3, 5, 5, 9, 19, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709280 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 Building ZINC001285709280 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709280 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 513) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709280 none C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 22, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 22, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 514) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709280 none C[C@@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 3, 5, 5, 9, 19, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709280 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709280 Building ZINC001285709281 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709281 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/515 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709281 none C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/516 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709281 none C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 2, 4, 4, 8, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 50, 50, 50, 50, 50, 50, 50, 2, 2, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709281 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 Building ZINC001285709281 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709281 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 515) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709281 none C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 516) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709281 none C[C@@H](CNC(=O)[C@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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, 2, 4, 4, 8, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 50, 50, 50, 50, 50, 50, 50, 2, 2, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709281 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709281 Building ZINC001285709282 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709282 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/517 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709282 none C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [3, 2, 3, 3, 7, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/518 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709282 none C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709282 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 Building ZINC001285709282 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285709282 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 517) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285709282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285709282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709282 none C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [3, 2, 3, 3, 7, 17, 17, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 17, 50, 50, 50, 50, 50, 50, 50, 2, 2, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 518) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285709282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285709282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285709282 none C[C@H](CNC(=O)[C@@H]1CCc2nncn2C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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: [7, 3, 7, 7, 12, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 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: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285709282 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285709282 Building ZINC001285715987 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285715987 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/519 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285715987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285715987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715987 none C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 22, 22, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/520 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285715987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285715987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715987 none C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285715987 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 Building ZINC001285715987 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285715987 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 519) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285715987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285715987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715987 none C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 22, 22, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 520) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285715987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285715987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715987 none C[C@@H](CNC(=O)[C@@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285715987 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715987 Building ZINC001285715988 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285715988 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/521 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285715988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285715988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715988 none C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/522 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285715988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285715988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715988 none C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285715988 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 Building ZINC001285715988 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285715988 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 521) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285715988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285715988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715988 none C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 21, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 522) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285715988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285715988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285715988 none C[C@@H](CNC(=O)[C@H]1CCc2nccn2C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285715988 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285715988 Building ZINC001285716053 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716053 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/523 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716053 none C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/524 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716053 none C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716053 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 Building ZINC001285716053 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716053 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 523) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716053 none C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 524) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716053 none C[C@@H](CNC(=O)C(C)(C)N1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 49, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716053 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716053 Building ZINC001285716054 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716054 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/525 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716054 none C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 7, 7, 7, 20, 20, 38, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/526 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716054 none C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 9, 9, 9, 22, 23, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 22, 22, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716054 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 Building ZINC001285716054 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716054 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 525) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716054 none C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 7, 7, 7, 20, 20, 38, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 7, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 526) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716054 none C[C@@H](CNC(=O)CCOC1CCOCC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 9, 9, 9, 22, 23, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 22, 22, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716054 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716054 Building ZINC001285716055 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716055 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/527 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716055 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 15, 15, 15, 48, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 41, 41, 50, 50, 50, 50, 50, 50, 50, 2, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/528 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716055 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 18, 45, 45, 50, 50, 50, 50, 50, 50, 50, 2, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716055 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 Building ZINC001285716055 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716055 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 527) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716055 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 15, 15, 15, 48, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 41, 41, 50, 50, 50, 50, 50, 50, 50, 2, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 528) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716055 none C[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 18, 45, 45, 50, 50, 50, 50, 50, 50, 50, 2, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716055 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716055 Building ZINC001285716056 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716056 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/529 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716056 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 11, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 20, 43, 43, 50, 50, 50, 50, 50, 50, 50, 2, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/530 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716056 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716056 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 Building ZINC001285716056 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716056 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 529) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716056 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 11, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 20, 43, 43, 50, 50, 50, 50, 50, 50, 50, 2, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 530) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716056 none C[C@@H](CNC(=O)C[C@H]1CCC(=O)N1C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 7, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 44, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716056 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716056 Building ZINC001285716072 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716072 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/531 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716072 none CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 46, 34, 46, 33, 33, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 46, 46, 46, 33, 19, 19, 8, 8, 8, 2, 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: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/532 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716072 none CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 36, 48, 35, 35, 15, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 48, 48, 48, 48, 35, 15, 15, 5, 5, 5, 2, 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: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716072 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 Building ZINC001285716072 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716072 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 531) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716072 none CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 46, 34, 46, 33, 33, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 46, 46, 46, 46, 46, 46, 33, 19, 19, 8, 8, 8, 2, 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: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 532) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716072 none CC(=O)N1CCC[C@H]1C(=O)NC[C@H](C)NC(=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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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, 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, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 36, 48, 35, 35, 15, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 48, 48, 48, 48, 35, 15, 15, 5, 5, 5, 2, 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: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716072 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716072 Building ZINC001285716073 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716073 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/533 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716073 none C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 21, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/534 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716073 none C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 37, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716073 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 Building ZINC001285716073 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716073 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 533) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716073 none C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 21, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 534) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716073 none C[C@@H](CNC(=O)c1cnc2n1CCOC2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 37, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716073 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716073 Building ZINC001285716079 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716079 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/535 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716079 none C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 15, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/536 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716079 none C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 24, 24, 34, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716079 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 Building ZINC001285716079 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716079 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 535) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716079 none C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 15, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 536) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716079 none C[C@@H](CNC(=O)[C@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 24, 24, 34, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716079 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716079 Building ZINC001285716080 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716080 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/537 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716080 none C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/538 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716080 none C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716080 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 Building ZINC001285716080 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716080 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 537) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716080 none C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 14, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 538) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285716080 none C[C@@H](CNC(=O)[C@@]1(C)CCC(=O)NC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 29, 29, 35, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716080 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716080 Building ZINC001285716144 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716144 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/539 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716144 none C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 18, 34, 34, 34, 43, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 34, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/540 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716144 none C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 31, 31, 31, 43, 46, 50, 46, 50, 50, 48, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 31, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716144 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 Building ZINC001285716144 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716144 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 539) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716144 none C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 18, 34, 34, 34, 43, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 34, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 540) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716144 none C[C@@H](CNC(=O)CNC(=O)c1ccncc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 31, 31, 31, 43, 46, 50, 46, 50, 50, 48, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 31, 43, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716144 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716144 Building ZINC001285716175 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716175 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/541 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716175 none C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 20, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 42, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/542 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716175 none C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 40, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716175 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 Building ZINC001285716175 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716175 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 541) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716175 none C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 20, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 42, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 542) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716175 none C[C@@H](CNC(=O)c1cccc2nn[nH]c21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 18, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 40, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716175 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716175 Building ZINC001285716228 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716228 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/543 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716228 none Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 32, 50, 26, 26, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/544 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716228 none Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 14, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716228 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 Building ZINC001285716228 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716228 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 543) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716228 none Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 32, 50, 26, 26, 16, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 544) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716228 none Cc1ncc2n1CC[C@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [50, 49, 41, 42, 43, 44, 45, 14, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/3016/xbk-8058097.37/working/building/ZINC001285716228 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716228 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716228 Building ZINC001285716230 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716230 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/545 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716230 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 25, 25, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/546 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716230 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 24, 24, 12, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 12, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716230 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 Building ZINC001285716230 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716230 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 545) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716230 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 25, 25, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 546) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001285716230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285716230 none Cc1ncc2n1CC[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 24, 24, 12, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 12, 12, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716230 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716230 Building ZINC001285716248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/547 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285716248 none C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 19, 19, 19, 35, 35, 35, 35, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 19, 35, 50, 50, 50, 50, 35, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/548 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285716248 none C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 24, 24, 24, 35, 35, 35, 35, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 24, 35, 50, 50, 50, 50, 35, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 Building ZINC001285716248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 547) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285716248 none C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 19, 19, 19, 35, 35, 35, 35, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 19, 35, 50, 50, 50, 50, 35, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 548) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285716248 none C[C@@H](CNC(=O)c1cnn(CCF)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 5, 5, 15, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 13, 24, 24, 24, 35, 35, 35, 35, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 24, 35, 50, 50, 50, 50, 35, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716248 Building ZINC001285716529 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716529 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/549 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716529 none C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 21, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/550 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716529 none C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 20, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716529 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 Building ZINC001285716529 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716529 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 549) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716529 none C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 21, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 550) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716529 none C[C@@H](CNC(=O)c1nnn(C(C)(C)C)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 20, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 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: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716529 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716529 Building ZINC001285716559 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716559 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/551 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001285716559 none C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 46, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/552 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001285716559 none C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 45, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716559 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 Building ZINC001285716559 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716559 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 551) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001285716559 none C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 46, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 552) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001285716559 none C[C@@H](CNC(=O)c1ccc2nn[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 45, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716559 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716559 Building ZINC001285716787 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285716787 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/553 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/554 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/555 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/555' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/556 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/556' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716787 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 Building ZINC001285716787 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285716787 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 553) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 554) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 555) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 556) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716787 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 Building ZINC001285716787 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285716787 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 553) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 554) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 555) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 556) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716787 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 Building ZINC001285716787 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285716787 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 553) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 554) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 48, 37, 37, 20, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 20, 20, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 555) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 556) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001285716787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285716787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285716787 none CC[C@@H]1[C@@H](C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 50, 38, 38, 19, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 19, 19, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716787 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716787 Building ZINC001285716807 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716807 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/557 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716807 none C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 47, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/558 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716807 none C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 26, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 46, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716807 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 Building ZINC001285716807 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716807 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 557) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716807 none C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 29, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 47, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 558) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285716807 none C[C@@H](CNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 26, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 46, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716807 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716807 Building ZINC001285716816 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716816 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/559 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716816 none C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 22, 44, 44, 44, 46, 46, 46, 46, 50, 50, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 44, 46, 46, 50, 50, 50, 50, 50, 50, 46, 2, 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/560 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716816 none C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 26, 46, 46, 46, 48, 48, 48, 48, 50, 50, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 46, 48, 48, 50, 50, 50, 50, 50, 50, 48, 2, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716816 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 Building ZINC001285716816 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716816 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 559) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716816 none C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 22, 44, 44, 44, 46, 46, 46, 46, 50, 50, 46, 46, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 44, 46, 46, 50, 50, 50, 50, 50, 50, 46, 2, 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 560) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285716816 none C[C@@H](CNC(=O)c1ccc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 26, 46, 46, 46, 48, 48, 48, 48, 50, 50, 48, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 46, 48, 48, 50, 50, 50, 50, 50, 50, 48, 2, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716816 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716816 Building ZINC001285716818 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716818 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/561 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285716818 none C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/562 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285716818 none C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 23, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716818 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 Building ZINC001285716818 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285716818 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 561) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285716818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285716818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285716818 none C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 24, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 562) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285716818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285716818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285716818 none C[C@@H](CNC(=O)c1ccnc2c1ncn2C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 23, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285716818 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285716818 Building ZINC001285717197 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717197 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/563 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717197 none C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 18, 35, 35, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/564 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717197 none C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 26, 26, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717197 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 Building ZINC001285717197 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717197 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 563) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717197 none C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 18, 35, 35, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 35, 47, 47, 47, 47, 47, 47, 50, 50, 47, 47, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 564) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717197 none C[C@@H](CNC(=O)[C@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 26, 26, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717197 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717197 Building ZINC001285717198 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717198 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/565 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717198 none C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 18, 34, 34, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/566 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717198 none C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 29, 29, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717198 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 Building ZINC001285717198 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717198 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 565) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717198 none C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 18, 34, 34, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 566) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717198 none C[C@@H](CNC(=O)[C@@H]1CCCN(C(N)=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 29, 29, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717198 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717198 Building ZINC001285717232 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717232 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/567 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001285717232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285717232 none Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 35, 35, 35, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 35, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 200 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/568 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001285717232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285717232 none Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 39, 39, 39, 17, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 39, 17, 17, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717232 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 Building ZINC001285717232 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717232 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 567) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001285717232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285717232 none Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 35, 35, 35, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 35, 15, 15, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 200 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 568) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001285717232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285717232 none Cc1cccn(CC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 39, 39, 39, 17, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 39, 17, 17, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717232 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717232 Building ZINC001285717393 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717393 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/569 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717393 none C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 34, 34, 34, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 34, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/570 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717393 none C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 30, 30, 30, 35, 35, 35, 35, 50, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 30, 35, 35, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717393 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 Building ZINC001285717393 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717393 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 569) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717393 none C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 17, 34, 34, 34, 36, 36, 36, 36, 50, 50, 50, 36, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 34, 36, 36, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 570) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717393 none C[C@@H](CNC(=O)c1ccn(CC(F)F)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 17, 30, 30, 30, 35, 35, 35, 35, 50, 50, 50, 35, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 30, 35, 35, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717393 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717393 Building ZINC001285717409 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717409 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/571 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285717409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285717409 none Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 24, 24, 24, 13, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 40, 40, 24, 13, 13, 7, 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: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/572 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285717409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285717409 none Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 44, 39, 18, 18, 18, 10, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 44, 39, 39, 18, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717409 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 Building ZINC001285717409 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717409 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 571) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285717409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285717409 none Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 40, 24, 24, 24, 13, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 40, 40, 24, 13, 13, 7, 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: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 572) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285717409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285717409 none Cc1nccc(CCC(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 44, 39, 18, 18, 18, 10, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 44, 39, 39, 18, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717409 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717409 Building ZINC001285717417 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717417 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/573 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717417 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 21, 39, 21, 21, 18, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 18, 18, 11, 11, 11, 4, 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: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/574 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717417 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 20, 44, 20, 20, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 16, 16, 8, 8, 8, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717417 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 Building ZINC001285717417 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717417 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 573) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717417 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 21, 39, 21, 21, 18, 11, 4, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 18, 18, 11, 11, 11, 4, 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: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 574) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717417 none CC[C@@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 20, 44, 20, 20, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 16, 16, 8, 8, 8, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717417 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717417 Building ZINC001285717418 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717418 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/575 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717418 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 25, 45, 25, 25, 20, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 20, 20, 13, 13, 13, 4, 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: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/576 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717418 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 25, 43, 25, 25, 18, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 25, 18, 18, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717418 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 Building ZINC001285717418 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717418 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 575) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717418 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 25, 45, 25, 25, 20, 13, 4, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 20, 20, 13, 13, 13, 4, 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: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 576) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285717418 none CC[C@H]1CCCN1C(=O)C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 25, 43, 25, 25, 18, 9, 3, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 25, 18, 18, 9, 9, 9, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717418 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717418 Building ZINC001285717911 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717911 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/577 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717911 none C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 10, 10, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 46, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 325 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/578 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717911 none C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 8, 8, 25, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 46, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717911 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 Building ZINC001285717911 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285717911 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 577) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285717911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285717911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717911 none C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 10, 10, 28, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 46, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 325 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 578) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285717911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285717911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001285717911 none C[C@@H](CNC(=O)c1ccc2nc(O)[nH]c2n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 8, 8, 25, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 46, 50, 50, 150, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285717911 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285717911 Building ZINC001285720820 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720820 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/579 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720820 none CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 17, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/580 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720820 none CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 23, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720820 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 Building ZINC001285720820 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720820 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 579) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720820 none CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 17, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 580) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720820 none CC[C@@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 23, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720820 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720820 Building ZINC001285720821 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720821 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/581 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720821 none CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 26, 26, 10, 5, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 10, 10, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 47, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/582 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720821 none CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 17, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720821 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 Building ZINC001285720821 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720821 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 581) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720821 none CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 26, 26, 10, 5, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 10, 10, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 47, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 582) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720821 none CC[C@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 17, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720821 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720821 Building ZINC001285720822 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720822 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/583 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720822 none CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 15, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 15, 15, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/584 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720822 none CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720822 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 Building ZINC001285720822 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720822 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 583) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720822 none CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 15, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 15, 15, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 584) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720822 none CC[C@]1(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720822 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720822 Building ZINC001285720823 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720823 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/585 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720823 none CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 21, 21, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/586 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720823 none CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 14, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 14, 14, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720823 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 Building ZINC001285720823 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285720823 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 585) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285720823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720823 none CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 21, 21, 9, 5, 3, 5, 5, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 586) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O) `ZINC001285720823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285720823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285720823 none CC[C@@]1(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 14, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 14, 14, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285720823 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285720823 Building ZINC001285721924 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285721924 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/587 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285721924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285721924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721924 none C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/588 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285721924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285721924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721924 none C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 47, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285721924 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 Building ZINC001285721924 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285721924 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 587) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285721924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285721924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721924 none C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 588) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285721924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285721924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721924 none C[C@@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 47, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285721924 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721924 Building ZINC001285721925 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285721925 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/589 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285721925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285721925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721925 none C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 48, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/590 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285721925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285721925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721925 none C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285721925 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 Building ZINC001285721925 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285721925 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 589) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285721925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285721925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721925 none C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 48, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 590) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285721925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285721925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285721925 none C[C@H](CNC(=O)c1cccc(C(N)=O)n1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285721925 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285721925 Building ZINC001285730660 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285730660 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/591 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1) `ZINC001285730660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285730660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285730660 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 25, 35, 35, 25, 25, 50, 50, 35, 35, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 50, 50, 35, 35] 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]) total number of confs: 233 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/592 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1) `ZINC001285730660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285730660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285730660 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 35, 35, 23, 23, 50, 50, 35, 35, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 50, 50, 35, 35] 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]) total number of confs: 233 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285730660 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 Building ZINC001285730660 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285730660 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 591) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1) `ZINC001285730660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285730660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285730660 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 25, 35, 35, 25, 25, 50, 50, 35, 35, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 50, 50, 35, 35] 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]) total number of confs: 233 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 592) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1) `ZINC001285730660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285730660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285730660 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc(C(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 35, 35, 23, 23, 50, 50, 35, 35, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 50, 50, 35, 35] 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]) total number of confs: 233 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285730660 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285730660 Building ZINC001285731854 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285731854 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/593 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285731854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285731854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285731854 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/594 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285731854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285731854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285731854 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285731854 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 Building ZINC001285731854 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285731854 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 593) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285731854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285731854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285731854 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 594) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21) `ZINC001285731854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285731854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285731854 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285731854 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285731854 Building ZINC001285734752 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285734752 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/595 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285734752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285734752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734752 none C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 37, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/596 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285734752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285734752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734752 none C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 49, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285734752 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 Building ZINC001285734752 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285734752 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 595) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285734752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285734752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734752 none C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 37, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 596) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285734752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285734752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734752 none C[C@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 49, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285734752 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734752 Building ZINC001285734754 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285734754 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/597 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285734754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285734754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734754 none C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/598 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285734754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285734754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734754 none C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 37, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285734754 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 Building ZINC001285734754 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285734754 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 597) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285734754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285734754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734754 none C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 598) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285734754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285734754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285734754 none C[C@@H](CNC(=O)c1cccc2ncnn21)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 37, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285734754 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285734754 Building ZINC001285737242 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285737242 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/599 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285737242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285737242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737242 none C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 20, 20, 20, 43, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 20, 43, 43, 47, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/600 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285737242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285737242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737242 none C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 22, 22, 22, 43, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 22, 43, 43, 47, 47, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285737242 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 Building ZINC001285737242 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285737242 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 599) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285737242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285737242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737242 none C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 20, 20, 20, 43, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 20, 43, 43, 47, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 600) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285737242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285737242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737242 none C[C@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 22, 22, 22, 43, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 22, 43, 43, 47, 47, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285737242 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737242 Building ZINC001285737244 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285737244 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/601 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285737244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285737244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737244 none C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 13, 22, 22, 22, 42, 47, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 42, 42, 47, 47, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/602 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285737244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285737244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737244 none C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 18, 18, 18, 44, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 18, 44, 44, 48, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285737244 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 Building ZINC001285737244 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285737244 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 601) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285737244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285737244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737244 none C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 13, 22, 22, 22, 42, 47, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 22, 42, 42, 47, 47, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 602) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285737244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285737244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285737244 none C[C@@H](CNC(=O)CCc1cn(C)nn1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 5, 8, 8, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 18, 18, 18, 44, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 18, 44, 44, 48, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285737244 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285737244 Building ZINC001285738631 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285738631 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/603 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1) `ZINC001285738631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285738631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285738631 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/604 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1) `ZINC001285738631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285738631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285738631 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285738631 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 Building ZINC001285738631 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285738631 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 603) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1) `ZINC001285738631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285738631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285738631 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 604) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1) `ZINC001285738631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285738631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285738631 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1nnn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285738631 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285738631 Building ZINC001285742387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/605 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742387 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 13, 23, 23, 26, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/606 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742387 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 6, 6, 11, 25, 25, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 Building ZINC001285742387 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742387 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 605) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742387 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 13, 23, 23, 26, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 606) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742387 none C[C@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 6, 6, 11, 25, 25, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742387 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742387 Building ZINC001285742388 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742388 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/607 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742388 none C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 6, 6, 11, 25, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/608 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742388 none C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 13, 23, 23, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742388 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 Building ZINC001285742388 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742388 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 607) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742388 none C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 6, 6, 11, 25, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 608) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742388 none C[C@@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 13, 23, 23, 27, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742388 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742388 Building ZINC001285742389 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742389 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/609 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742389 none C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 14, 30, 30, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/610 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742389 none C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 7, 17, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742389 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 Building ZINC001285742389 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742389 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 609) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742389 none C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 5, 5, 14, 30, 30, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 610) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742389 none C[C@@H](CNC(=O)[C@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 7, 17, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742389 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742389 Building ZINC001285742390 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742390 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/611 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742390 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 16, 35, 35, 38, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/612 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742390 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 4, 12, 28, 28, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742390 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 Building ZINC001285742390 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742390 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 611) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285742390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742390 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 6, 6, 16, 35, 35, 38, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 612) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285742390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285742390 none C[C@H](CNC(=O)[C@@H]1CCN(C)C(=O)C1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 4, 12, 28, 28, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 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, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742390 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742390 Building ZINC001285742425 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742425 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/613 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1) `ZINC001285742425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742425 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 20, 20, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/614 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1) `ZINC001285742425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742425 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 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/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742425 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 Building ZINC001285742425 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742425 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 613) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1) `ZINC001285742425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742425 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 20, 20, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 614) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1) `ZINC001285742425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742425 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 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/3016/xbk-8058097.37/working/building/ZINC001285742425 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742425 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742425 Building ZINC001285742426 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742426 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/615 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1) `ZINC001285742426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742426 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/616 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1) `ZINC001285742426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742426 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742426 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 Building ZINC001285742426 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285742426 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 615) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1) `ZINC001285742426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285742426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742426 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 21, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 616) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1) `ZINC001285742426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285742426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285742426 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCc2ncncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 21, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285742426 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285742426 Building ZINC001285744714 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285744714 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/617 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285744714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285744714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285744714 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [30, 13, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/618 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285744714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285744714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285744714 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285744714 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 Building ZINC001285744714 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285744714 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 617) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285744714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285744714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285744714 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [30, 13, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 618) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1) `ZINC001285744714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285744714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001285744714 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2nc[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 6, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285744714 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285744714 Building ZINC001285747260 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285747260 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/619 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2) `ZINC001285747260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285747260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285747260 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/620 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2) `ZINC001285747260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285747260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285747260 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285747260 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 Building ZINC001285747260 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285747260 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 619) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2) `ZINC001285747260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285747260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285747260 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 620) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2) `ZINC001285747260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285747260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285747260 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285747260 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285747260 Building ZINC001285751207 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285751207 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/621 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285751207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285751207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285751207 none CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 32, 32, 32, 19, 11, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 50, 50, 50, 50, 32, 19, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47] 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, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/622 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285751207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285751207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285751207 none CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 30, 30, 30, 21, 9, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 30, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46] 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, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285751207 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 Building ZINC001285751207 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285751207 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 621) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285751207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285751207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285751207 none CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 32, 32, 32, 19, 11, 19, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 50, 50, 50, 50, 32, 19, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47] 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, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 622) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1) `ZINC001285751207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285751207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001285751207 none CC(=O)NC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 30, 30, 30, 21, 9, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 30, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46] 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, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285751207 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285751207 Building ZINC001285754262 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285754262 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/623 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285754262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754262 none CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 21, 21, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/624 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285754262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754262 none CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 18, 8, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285754262 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 Building ZINC001285754262 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285754262 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 623) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285754262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754262 none CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 21, 21, 12, 6, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 624) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285754262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754262 none CC(=O)N1CCC[C@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 50, 23, 23, 18, 8, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285754262 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754262 Building ZINC001285754264 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285754264 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/625 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285754264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754264 none CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 49, 19, 19, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 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: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/626 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285754264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754264 none CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 18, 7, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285754264 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 Building ZINC001285754264 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285754264 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 625) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@@H](C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285754264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754264 none CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 49, 19, 19, 10, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 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: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 626) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@@H](C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285754264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285754264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285754264 none CC(=O)N1CCC[C@@H](C(=O)N[C@@H](C)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 50, 22, 22, 18, 7, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285754264 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285754264 Building ZINC001285755616 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755616 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/627 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285755616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755616 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 29, 29, 29, 47, 47, 47, 47, 47, 47, 50, 50, 47, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 47, 47, 47, 47, 47, 47, 50, 50, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/628 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285755616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755616 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755616 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 Building ZINC001285755616 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755616 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 627) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285755616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755616 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 29, 29, 29, 47, 47, 47, 47, 47, 47, 50, 50, 47, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 47, 47, 47, 47, 47, 47, 50, 50, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 628) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1) `ZINC001285755616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755616 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755616 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755616 Building ZINC001285755621 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755621 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/629 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285755621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755621 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/630 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285755621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755621 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755621 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 Building ZINC001285755621 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755621 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 629) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285755621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755621 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 630) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1) `ZINC001285755621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285755621 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCN(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 26, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755621 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755621 Building ZINC001285755760 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755760 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/631 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001285755760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285755760 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/632 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001285755760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285755760 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755760 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 Building ZINC001285755760 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285755760 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 631) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001285755760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285755760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285755760 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 632) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001285755760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285755760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285755760 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 11, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285755760 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285755760 Building ZINC001285758777 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285758777 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/633 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285758777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285758777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758777 none C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 25, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/634 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285758777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285758777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758777 none C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285758777 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 Building ZINC001285758777 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285758777 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 633) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285758777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285758777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758777 none C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 25, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 44, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 634) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285758777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285758777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758777 none C[C@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285758777 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758777 Building ZINC001285758778 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285758778 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/635 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285758778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285758778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758778 none C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/636 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285758778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285758778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758778 none C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 46, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285758778 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 Building ZINC001285758778 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285758778 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 635) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285758778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285758778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758778 none C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 636) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285758778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285758778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285758778 none C[C@@H](CNC(=O)c1cn(C)ccc1=O)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 26, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 46, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285758778 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285758778 Building ZINC001285759969 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285759969 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/637 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1) `ZINC001285759969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285759969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285759969 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 29, 34, 43, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 29, 29, 43, 43, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/638 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1) `ZINC001285759969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285759969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285759969 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 29, 33, 46, 50, 50, 50, 50, 50, 11, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 29, 29, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285759969 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 Building ZINC001285759969 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285759969 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 637) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1) `ZINC001285759969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285759969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285759969 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 29, 34, 43, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 29, 29, 43, 43, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 638) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1) `ZINC001285759969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285759969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001285759969 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 29, 33, 46, 50, 50, 50, 50, 50, 11, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 29, 29, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285759969 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285759969 Building ZINC001285760655 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285760655 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/639 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2) `ZINC001285760655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285760655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285760655 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 12, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/640 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2) `ZINC001285760655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285760655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285760655 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285760655 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 Building ZINC001285760655 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285760655 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 639) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2) `ZINC001285760655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285760655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285760655 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 12, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 640) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2) `ZINC001285760655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285760655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285760655 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2n(n1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285760655 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285760655 Building ZINC001285761084 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285761084 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/641 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21) `ZINC001285761084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285761084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285761084 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 35, 36, 38, 37, 39, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/642 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21) `ZINC001285761084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285761084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285761084 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285761084 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 Building ZINC001285761084 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285761084 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 641) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21) `ZINC001285761084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285761084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285761084 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 35, 36, 38, 37, 39, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 642) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21) `ZINC001285761084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285761084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285761084 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285761084 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285761084 Building ZINC001285762784 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285762784 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/643 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C) `ZINC001285762784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285762784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285762784 none Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 32, 32, 22, 12, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 32, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 100 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]) total number of confs: 253 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/644 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C) `ZINC001285762784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285762784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285762784 none Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 25, 11, 25, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 37, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 100 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]) total number of confs: 263 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285762784 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 Building ZINC001285762784 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285762784 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 643) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C) `ZINC001285762784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285762784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285762784 none Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 32, 32, 22, 12, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 32, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 100 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]) total number of confs: 253 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 644) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C) `ZINC001285762784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285762784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285762784 none Cc1nnc(O)c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 25, 11, 25, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 37, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 100 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]) total number of confs: 263 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285762784 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285762784 Building ZINC001285776479 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285776479 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/645 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285776479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285776479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776479 none C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 9, 15, 15, 15, 46, 48, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 46, 46, 48, 48, 50, 50, 50, 50, 50, 3, 3, 3, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/646 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285776479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285776479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776479 none C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 18, 18, 18, 45, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 18, 45, 45, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285776479 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 Building ZINC001285776479 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285776479 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 645) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285776479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285776479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776479 none C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 9, 15, 15, 15, 46, 48, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 15, 46, 46, 48, 48, 50, 50, 50, 50, 50, 3, 3, 3, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 646) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285776479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285776479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776479 none C[C@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 18, 18, 18, 45, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 18, 45, 45, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285776479 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776479 Building ZINC001285776481 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285776481 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/647 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285776481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285776481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776481 none C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 18, 18, 18, 45, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 18, 45, 45, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/648 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285776481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285776481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776481 none C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 9, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 46, 46, 48, 48, 50, 50, 50, 50, 50, 3, 3, 3, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285776481 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 Building ZINC001285776481 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285776481 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 647) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285776481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285776481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776481 none C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 10, 18, 18, 18, 45, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 18, 45, 45, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 648) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285776481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285776481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285776481 none C[C@@H](CNC(=O)CCc1cncn1C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 9, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 46, 46, 48, 48, 50, 50, 50, 50, 50, 3, 3, 3, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285776481 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285776481 Building ZINC001285777113 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285777113 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/649 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285777113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285777113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777113 none C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 24, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/650 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285777113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285777113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777113 none C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 11, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 23, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285777113 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 Building ZINC001285777113 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285777113 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 649) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285777113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285777113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777113 none C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 13, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 24, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 650) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285777113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285777113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777113 none C[C@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 11, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 23, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285777113 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777113 Building ZINC001285777115 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285777115 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/651 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285777115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285777115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777115 none C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 22, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/652 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285777115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285777115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777115 none C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 13, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 25, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285777115 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 Building ZINC001285777115 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285777115 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 651) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285777115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285777115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777115 none C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 22, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 652) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285777115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285777115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285777115 none C[C@@H](CNC(=O)c1nccn2ccnc12)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 13, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 25, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285777115 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285777115 Building ZINC001285780527 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285780527 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/653 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1) `ZINC001285780527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285780527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285780527 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 13, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/654 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1) `ZINC001285780527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285780527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285780527 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 14, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285780527 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 Building ZINC001285780527 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285780527 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 653) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1) `ZINC001285780527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285780527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285780527 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 13, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 654) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1) `ZINC001285780527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285780527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285780527 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccc2ncn(C)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 14, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285780527 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285780527 Building ZINC001285782346 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285782346 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/655 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285782346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782346 none CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 41, 41, 41, 30, 41, 23, 23, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 41, 41, 41, 41, 41, 41, 23, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 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: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/656 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285782346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782346 none CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 33, 46, 22, 22, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 46, 46, 46, 46, 46, 46, 46, 22, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285782346 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 Building ZINC001285782346 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285782346 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 655) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285782346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782346 none CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 41, 41, 41, 30, 41, 23, 23, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 41, 41, 41, 41, 41, 41, 23, 14, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 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: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 656) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285782346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782346 none CC(=O)N1CC[C@@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 33, 46, 22, 22, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 46, 46, 46, 46, 46, 46, 46, 22, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285782346 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782346 Building ZINC001285782347 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285782347 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/657 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285782347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782347 none CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 29, 46, 21, 21, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 46, 46, 46, 46, 46, 46, 46, 21, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 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: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/658 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285782347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782347 none CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 26, 26, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285782347 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 Building ZINC001285782347 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285782347 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 657) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CC[C@](C)(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285782347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782347 none CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 29, 46, 21, 21, 15, 9, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 46, 46, 46, 46, 46, 46, 46, 21, 15, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 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: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 658) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CC[C@](C)(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285782347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285782347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285782347 none CC(=O)N1CC[C@](C)(C(=O)N[C@@H](C)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 38, 50, 26, 26, 18, 10, 18, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285782347 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285782347 Building ZINC001285783026 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285783026 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/659 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn21) `ZINC001285783026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285783026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285783026 none Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 37, 37, 24, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/660 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn21) `ZINC001285783026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285783026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285783026 none Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 29, 11, 29, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285783026 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 Building ZINC001285783026 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285783026 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 659) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn21) `ZINC001285783026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285783026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285783026 none Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 37, 37, 24, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 660) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn21) `ZINC001285783026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285783026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285783026 none Cc1ccnc2nc(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 29, 11, 29, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 38, 29, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285783026 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285783026 Building ZINC001285784390 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285784390 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/661 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)nn1C) `ZINC001285784390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285784390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285784390 none COc1c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 30, 12, 30, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 30, 30, 30, 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, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/662 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)nn1C) `ZINC001285784390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285784390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285784390 none COc1c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 47, 47, 32, 12, 32, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 32, 32, 32, 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, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285784390 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 Building ZINC001285784390 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285784390 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 661) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)nn1C) `ZINC001285784390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285784390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285784390 none COc1c(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c(C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 30, 12, 30, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 30, 30, 30, 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, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 662) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)nn1C) `ZINC001285784390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285784390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285784390 none COc1c(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c(C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 47, 47, 32, 12, 32, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 47, 32, 32, 32, 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, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285784390 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285784390 Building ZINC001285791430 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791430 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/663 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791430 none Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 29, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 33, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/664 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791430 none Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 31, 26, 26, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791430 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 Building ZINC001285791430 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791430 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 663) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791430 none Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 29, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 33, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 664) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791430 none Cn1cnc(C(=O)N[C@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 31, 26, 26, 26, 26, 26, 26, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791430 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791430 Building ZINC001285791431 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791431 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/665 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791431 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 27, 27, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/666 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791431 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 28, 28, 28, 28, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791431 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 Building ZINC001285791431 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791431 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 665) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791431 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 27, 27, 27, 27, 27, 27, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 666) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791431 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 28, 28, 28, 28, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791431 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791431 Building ZINC001285791432 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791432 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/667 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791432 none Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 30, 30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/668 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791432 none Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 20, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791432 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 Building ZINC001285791432 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791432 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 667) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791432 none Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 38, 38, 30, 30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 38, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 668) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791432 none Cn1cnc(C(=O)N[C@H]2CCCC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 20, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791432 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791432 Building ZINC001285791433 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791433 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/669 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791433 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 20, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/670 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791433 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 41, 33, 33, 33, 33, 33, 33, 33, 20, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791433 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 Building ZINC001285791433 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285791433 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 669) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285791433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791433 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 20, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 670) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285791433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285791433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285791433 none Cn1cnc(C(=O)N[C@@H]2CCCC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 41, 33, 33, 33, 33, 33, 33, 33, 20, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285791433 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285791433 Building ZINC001285813221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285813221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/671 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285813221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285813221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813221 none C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 11, 11, 11, 15, 12, 12, 30, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 15, 30, 30, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/672 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285813221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285813221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813221 none C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 16, 16, 16, 20, 16, 16, 37, 49, 49, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 16, 20, 37, 37, 49, 49, 49, 50, 49, 2, 2, 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: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285813221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 Building ZINC001285813221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285813221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 671) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285813221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285813221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813221 none C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 11, 11, 11, 15, 12, 12, 30, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 11, 15, 30, 30, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 672) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285813221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285813221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813221 none C[C@@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 16, 16, 16, 20, 16, 16, 37, 49, 49, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 16, 20, 37, 37, 49, 49, 49, 50, 49, 2, 2, 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: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285813221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813221 Building ZINC001285813222 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285813222 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/673 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285813222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285813222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813222 none C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 14, 14, 14, 18, 15, 15, 34, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 18, 34, 34, 50, 50, 50, 50, 50, 2, 2, 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: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/674 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285813222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285813222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813222 none C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 12, 12, 12, 16, 12, 12, 34, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 16, 34, 34, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285813222 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 Building ZINC001285813222 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285813222 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 673) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285813222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285813222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813222 none C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 14, 14, 14, 18, 15, 15, 34, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 14, 18, 34, 34, 50, 50, 50, 50, 50, 2, 2, 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: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 674) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285813222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285813222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285813222 none C[C@H](CNC(=O)C(=O)NCC1CC1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 8, 12, 12, 12, 16, 12, 12, 34, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 12, 16, 34, 34, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 214 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285813222 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285813222 Building ZINC001285821271 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821271 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/675 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821271 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 11, 11, 6, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11, 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: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/676 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821271 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 14, 14, 6, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 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: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821271 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 Building ZINC001285821271 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821271 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 675) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821271 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 11, 11, 6, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11, 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: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 676) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821271 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 14, 14, 6, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 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: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821271 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821271 Building ZINC001285821272 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821272 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/677 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821272 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 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: 131 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/678 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821272 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 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: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821272 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 Building ZINC001285821272 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821272 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 677) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821272 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 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: 131 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 678) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821272 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 12, 12, 6, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 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: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821272 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821272 Building ZINC001285821273 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821273 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/679 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821273 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 20, 20, 20, 20, 20, 34, 34, 50, 50, 50, 50, 50, 20, 20, 5, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 20, 20, 50, 50, 50, 50, 20, 20, 20, 20, 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: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/680 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821273 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821273 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 Building ZINC001285821273 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821273 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 679) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821273 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 20, 20, 20, 20, 20, 34, 34, 50, 50, 50, 50, 50, 20, 20, 5, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 20, 20, 50, 50, 50, 50, 20, 20, 20, 20, 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: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 680) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821273 none CC[C@H]1CN(C(=O)c2cnnn2C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 142 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821273 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821273 Building ZINC001285821274 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821274 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/681 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821274 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/682 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821274 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 16, 16, 16, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821274 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 Building ZINC001285821274 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285821274 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 681) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285821274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285821274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821274 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 682) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285821274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285821274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001285821274 none CC[C@@H]1CN(C(=O)c2cnnn2C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 16, 16, 16, 32, 32, 50, 50, 50, 50, 50, 16, 16, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 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: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285821274 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285821274 Building ZINC001285843325 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285843325 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/683 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285843325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843325 none Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/684 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285843325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843325 none Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285843325 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 Building ZINC001285843325 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285843325 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 683) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285843325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843325 none Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 684) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285843325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843325 none Cc1cc(=O)c(C(=O)NC[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285843325 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843325 Building ZINC001285843326 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285843326 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/685 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285843326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843326 none Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 8, 8, 8, 3, 3, 3, 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/686 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285843326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843326 none Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285843326 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 Building ZINC001285843326 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285843326 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 685) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285843326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843326 none Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 8, 8, 8, 3, 3, 3, 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 686) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001285843326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285843326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285843326 none Cc1cc(=O)c(C(=O)NC[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 8, 3, 8, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 3, 3, 3, 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285843326 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285843326 Building ZINC001285845651 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845651 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/687 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/687' -> `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]1CCN1C(=O)CCOCC(F)F) `ZINC001285845651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845651 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 15, 15, 29, 29, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 29, 29, 29, 29, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/688 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/688' -> `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]1CCN1C(=O)CCOCC(F)F) `ZINC001285845651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845651 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 19, 19, 25, 25, 34, 34, 43, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 19, 19, 19, 34, 34, 34, 34, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845651 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 Building ZINC001285845651 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845651 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 687) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F) `ZINC001285845651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845651 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 15, 15, 29, 29, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 29, 29, 29, 29, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 688) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F) `ZINC001285845651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845651 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 19, 19, 19, 19, 25, 25, 34, 34, 43, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 19, 19, 19, 34, 34, 34, 34, 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845651 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845651 Building ZINC001285845654 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845654 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/689 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/689' -> `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]1CCN1C(=O)CCOCC(F)F) `ZINC001285845654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845654 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 26, 26, 35, 35, 43, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 20, 20, 35, 35, 35, 35, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/690 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/690' -> `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]1CCN1C(=O)CCOCC(F)F) `ZINC001285845654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845654 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 15, 15, 29, 29, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 29, 29, 29, 29, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845654 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 Building ZINC001285845654 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845654 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 689) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F) `ZINC001285845654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845654 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 26, 26, 35, 35, 43, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 20, 20, 20, 20, 35, 35, 35, 35, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 690) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F) `ZINC001285845654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845654 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CCOCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 14, 14, 14, 14, 14, 15, 15, 29, 29, 42, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 14, 14, 29, 29, 29, 29, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845654 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845654 Building ZINC001285845802 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845802 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/691 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/691' -> `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]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845802 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 41, 44, 44, 44, 44, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 44, 44, 44, 44, 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, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/692 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/692' -> `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]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845802 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 38, 44, 44, 44, 44, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 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, 48]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845802 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 Building ZINC001285845802 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845802 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 691) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845802 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 41, 44, 44, 44, 44, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 44, 44, 44, 44, 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, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 692) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845802 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 38, 44, 44, 44, 44, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 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, 48]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845802 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845802 Building ZINC001285845805 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845805 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/693 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/693' -> `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]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845805 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 38, 44, 44, 44, 44, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 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, 48]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/694 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/694' -> `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]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845805 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 41, 45, 45, 45, 45, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 45, 45, 45, 45, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845805 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 Building ZINC001285845805 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845805 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 693) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845805 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 38, 44, 44, 44, 44, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 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, 48]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 694) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2) `ZINC001285845805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285845805 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cn2c(n1)COCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 41, 45, 45, 45, 45, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 45, 45, 45, 45, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285845805 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845805 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845805 Building ZINC001285845806 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845806 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/695 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845806 none CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 23, 19, 23, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 19, 19, 19, 19, 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: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/696 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845806 none CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input 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, 26, 30, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845806 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 Building ZINC001285845806 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845806 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 695) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845806 none CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 23, 19, 23, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 19, 19, 19, 19, 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: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 696) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845806 none CN1CC[C@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input 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, 26, 30, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845806 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845806 Building ZINC001285845809 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845809 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/697 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845809 none CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input 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, 24, 28, 24, 24, 24, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 24, 24, 24, 24, 11, 11, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/698 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845809 none CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 23, 19, 23, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 19, 19, 19, 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: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845809 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 Building ZINC001285845809 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845809 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 697) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845809 none CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input 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, 24, 28, 24, 24, 24, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 24, 24, 24, 24, 11, 11, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 698) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845809 none CN1CC[C@@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 23, 19, 23, 19, 19, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 19, 19, 19, 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: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845809 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845809 Building ZINC001285845810 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845810 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/699 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845810 none CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 31, 26, 31, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/700 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845810 none CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 29, 24, 29, 24, 24, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 24, 24, 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: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845810 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 Building ZINC001285845810 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845810 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 699) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845810 none CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 31, 26, 31, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 700) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845810 none CN1CC[C@@H](CC(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 29, 24, 29, 24, 24, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 24, 24, 24, 24, 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: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845810 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845810 Building ZINC001285845813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/701 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845813 none CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 30, 26, 30, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 26, 26, 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: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/702 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845813 none CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 30, 25, 30, 25, 25, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 Building ZINC001285845813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285845813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 701) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285845813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845813 none CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 30, 26, 30, 26, 26, 26, 10, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 26, 26, 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: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 702) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001285845813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285845813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285845813 none CN1CC[C@H](CC(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 30, 25, 30, 25, 25, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285845813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285845813 Building ZINC001285846687 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285846687 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/703 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/703' -> `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]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285846687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846687 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 30, 30, 38, 38, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 221 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/704 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/704' -> `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]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285846687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846687 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 23, 32, 32, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 212 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285846687 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 Building ZINC001285846687 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285846687 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 703) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285846687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846687 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 30, 30, 38, 38, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 221 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 704) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285846687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846687 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 23, 32, 32, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 212 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285846687 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846687 Building ZINC001285846685 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285846685 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/705 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/705' -> `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]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285846685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846685 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 23, 32, 32, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 212 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/706 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/706' -> `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]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285846685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846685 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 20, 29, 29, 38, 38, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 223 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285846685 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 Building ZINC001285846685 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285846685 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 705) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285846685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846685 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 23, 32, 32, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 212 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 706) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O) `ZINC001285846685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285846685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285846685 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)C(C)(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 20, 29, 29, 38, 38, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 223 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285846685 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285846685 Building ZINC001285847105 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847105 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/707 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847105 none CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 24, 26, 24, 24, 24, 16, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 26, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 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: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/708 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847105 none CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 23, 29, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847105 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 Building ZINC001285847105 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847105 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 707) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847105 none CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 24, 26, 24, 24, 24, 16, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 26, 24, 24, 24, 24, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 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: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 708) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847105 none CCc1cc(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 23, 29, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847105 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847105 Building ZINC001285847107 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847107 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/709 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847107 none CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 23, 30, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 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: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/710 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847107 none CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 24, 26, 24, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 26, 24, 24, 24, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 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: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847107 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 Building ZINC001285847107 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847107 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 709) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847107 none CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 23, 30, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30] 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: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 710) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001285847107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285847107 none CCc1cc(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 24, 26, 24, 24, 24, 15, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 26, 24, 24, 24, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26] 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: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847107 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847107 Building ZINC001285847149 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847149 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/711 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/711' -> `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]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847149 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/712 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/712' -> `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]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847149 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847149 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 Building ZINC001285847149 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847149 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 711) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847149 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 24, 24, 24, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 712) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847149 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 23, 23, 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847149 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847149 Building ZINC001285847152 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847152 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/713 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/713' -> `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]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 24, 24, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 24, 24, 24, 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]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/714 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/714' -> `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]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847152 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 Building ZINC001285847152 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285847152 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 713) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285847152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 24, 24, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 24, 24, 24, 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]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 714) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1) `ZINC001285847152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285847152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285847152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1ccc2nnnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 21, 21, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285847152 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285847152 Building ZINC001285848391 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848391 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/715 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285848391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848391 none CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 39, 36, 37, 20, 17, 20, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 39, 39, 39, 39, 37, 37, 17, 17, 17, 17, 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: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/716 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285848391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848391 none CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 35, 33, 33, 18, 17, 18, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 35, 35, 35, 35, 33, 33, 17, 17, 17, 17, 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848391 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 Building ZINC001285848391 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848391 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 715) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285848391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848391 none CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 39, 36, 37, 20, 17, 20, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 39, 39, 39, 39, 37, 37, 17, 17, 17, 17, 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: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 716) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285848391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848391 none CNC(=O)CCCCC(=O)N1CC[C@@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 35, 33, 33, 18, 17, 18, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 35, 35, 35, 35, 33, 33, 17, 17, 17, 17, 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848391 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848391 Building ZINC001285848392 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848392 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/717 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285848392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848392 none CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 36, 34, 34, 19, 18, 19, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 36, 36, 36, 36, 34, 34, 18, 18, 18, 18, 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/718 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285848392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848392 none CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 38, 35, 36, 20, 17, 20, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 38, 38, 38, 38, 36, 36, 17, 17, 17, 17, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848392 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 Building ZINC001285848392 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848392 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 717) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285848392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848392 none CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 36, 34, 34, 19, 18, 19, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 43, 43, 36, 36, 36, 36, 34, 34, 18, 18, 18, 18, 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 718) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285848392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848392 none CNC(=O)CCCCC(=O)N1CC[C@H]1CNC(=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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 38, 35, 36, 20, 17, 20, 17, 17, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 38, 38, 38, 38, 36, 36, 17, 17, 17, 17, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848392 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848392 Building ZINC001285848938 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848938 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/719 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/719' -> `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]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848938 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 14, 33, 33, 33, 33, 33, 40, 40, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 33, 33, 33, 33, 49, 49, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/720 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/720' -> `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]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848938 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 12, 29, 29, 29, 29, 29, 33, 33, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 29, 29, 29, 46, 46, 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: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848938 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 Building ZINC001285848938 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848938 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 719) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848938 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 14, 33, 33, 33, 33, 33, 40, 40, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 33, 33, 33, 33, 49, 49, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 720) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848938 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 12, 29, 29, 29, 29, 29, 33, 33, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 29, 29, 29, 46, 46, 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: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848938 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848938 Building ZINC001285848940 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848940 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/721 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/721' -> `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]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848940 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 13, 29, 29, 29, 29, 29, 38, 38, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 46, 46, 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: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/722 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/722' -> `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]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848940 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 15, 31, 31, 31, 31, 31, 36, 36, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 31, 31, 31, 31, 47, 47, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848940 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 Building ZINC001285848940 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848940 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 721) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848940 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 13, 29, 29, 29, 29, 29, 38, 38, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 46, 46, 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: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 722) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1) `ZINC001285848940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285848940 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1C[C@H]1c1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 2, 2, 2, 15, 31, 31, 31, 31, 31, 36, 36, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 31, 31, 31, 31, 47, 47, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848940 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848940 Building ZINC001285848951 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848951 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/723 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848951 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 29, 34, 23, 29, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/724 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848951 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 35, 21, 27, 21, 21, 21, 15, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848951 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 Building ZINC001285848951 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848951 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 723) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848951 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 29, 34, 23, 29, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 724) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848951 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 35, 21, 27, 21, 21, 21, 15, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848951 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848951 Building ZINC001285848953 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848953 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/725 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848953 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 35, 18, 25, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/726 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848953 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 26, 36, 18, 26, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848953 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 Building ZINC001285848953 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848953 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 725) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848953 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 35, 18, 25, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 726) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848953 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 26, 36, 18, 26, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848953 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848953 Building ZINC001285848955 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848955 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/727 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848955 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 39, 24, 31, 24, 24, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/728 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848955 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 24, 34, 19, 24, 19, 19, 19, 16, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848955 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 Building ZINC001285848955 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848955 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 727) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848955 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 39, 24, 31, 24, 24, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 728) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848955 none C[C@H]1CCN(C(=O)C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 24, 34, 19, 24, 19, 19, 19, 16, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848955 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848955 Building ZINC001285848957 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848957 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/729 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848957 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 35, 18, 26, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/730 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848957 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 37, 18, 26, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848957 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 Building ZINC001285848957 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285848957 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 729) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285848957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848957 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 35, 18, 26, 18, 18, 18, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 730) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285848957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285848957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285848957 none C[C@@H]1CCN(C(=O)C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 26, 37, 18, 26, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285848957 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285848957 Building ZINC001285850139 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850139 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/731 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/731' -> `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]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 32, 33, 33, 33, 33, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 33, 33, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/732 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/732' -> `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]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 31, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850139 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 Building ZINC001285850139 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850139 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 731) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 32, 33, 33, 33, 33, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 33, 33, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 732) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 31, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850139 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850139 Building ZINC001285850140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/733 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/733' -> `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]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 31, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/734 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/734' -> `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]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 32, 33, 33, 33, 33, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 33, 33, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 Building ZINC001285850140 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850140 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 733) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 29, 31, 31, 31, 31, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 734) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1) `ZINC001285850140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)c1cnc2[nH]ncc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 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, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 32, 33, 33, 33, 33, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 33, 33, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850140 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850140 Building ZINC001285850155 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850155 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/735 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/735' -> `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]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850155 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 31, 31, 31, 31, 39, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/736 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/736' -> `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]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850155 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 28, 28, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850155 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 Building ZINC001285850155 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850155 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 735) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850155 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 31, 31, 31, 31, 31, 39, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 736) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850155 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 28, 28, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850155 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850155 Building ZINC001285850156 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850156 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/737 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/737' -> `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]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 24, 24, 34, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/738 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/738' -> `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]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850156 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 Building ZINC001285850156 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850156 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 737) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 24, 24, 34, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 738) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850156 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850156 Building ZINC001285850157 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850157 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/739 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/739' -> `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]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/740 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/740' -> `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]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 32, 32, 32, 32, 32, 39, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850157 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 Building ZINC001285850157 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850157 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 739) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 27, 27, 27, 27, 27, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 740) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001285850157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 32, 32, 32, 32, 32, 39, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850157 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850157 Building ZINC001285850158 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850158 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/741 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/741' -> `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]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850158 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 26, 26, 26, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/742 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/742' -> `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]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850158 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 33, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850158 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 Building ZINC001285850158 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850158 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 741) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850158 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 26, 26, 26, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 154 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 742) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001285850158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850158 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)[C@@H]1CCCc2nn[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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 23, 23, 23, 23, 23, 33, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850158 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850158 Building ZINC001285850159 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850159 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/743 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850159 none Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 33, 28, 33, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 28, 28, 28, 28, 13, 13, 2, 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/744 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850159 none Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 30, 26, 30, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 26, 26, 26, 26, 11, 11, 2, 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: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850159 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 Building ZINC001285850159 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850159 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 743) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850159 none Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 33, 28, 33, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 28, 28, 28, 28, 13, 13, 2, 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 744) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850159 none Cn1ccnc1CCC(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 30, 26, 30, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 26, 26, 26, 26, 11, 11, 2, 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: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850159 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850159 Building ZINC001285850160 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850160 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/745 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850160 none Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 30, 26, 30, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 26, 26, 26, 26, 11, 11, 2, 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: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/746 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850160 none Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 33, 28, 33, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 28, 28, 28, 28, 13, 13, 2, 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850160 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 Building ZINC001285850160 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850160 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 745) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850160 none Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 30, 26, 30, 26, 26, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 26, 26, 26, 26, 11, 11, 2, 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: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 746) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285850160 none Cn1ccnc1CCC(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 43, 33, 28, 33, 28, 28, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 43, 43, 28, 28, 28, 28, 13, 13, 2, 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850160 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850160 Building ZINC001285850173 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850173 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/747 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/747' -> `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]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850173 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 24, 24, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 46, 46, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/748 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/748' -> `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]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850173 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 17, 21, 21, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 45, 45, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850173 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 Building ZINC001285850173 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850173 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 747) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850173 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 20, 20, 24, 24, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 20, 20, 20, 46, 46, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 748) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850173 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 17, 21, 21, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 45, 45, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850173 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850173 Building ZINC001285850174 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850174 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/749 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/749' -> `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]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850174 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 18, 22, 22, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 18, 18, 18, 45, 45, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/750 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/750' -> `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]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850174 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 25, 25, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 46, 46, 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]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850174 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 Building ZINC001285850174 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850174 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 749) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850174 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 18, 18, 22, 22, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 18, 18, 18, 45, 45, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 750) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=O) `ZINC001285850174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850174 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CN1CCCCC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 21, 21, 21, 21, 21, 25, 25, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 21, 21, 21, 46, 46, 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]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850174 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850174 Building ZINC001285850323 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850323 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/751 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850323 none CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 39, 26, 39, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 26, 26, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/752 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850323 none CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 40, 28, 40, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850323 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 Building ZINC001285850323 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850323 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 751) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850323 none CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 39, 26, 39, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 26, 26, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 752) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850323 none CNC(=O)C1(C(=O)N2CC[C@@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 40, 28, 40, 28, 28, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850323 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850323 Building ZINC001285850325 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850325 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/753 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850325 none CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 38, 27, 38, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/754 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850325 none CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 45, 50, 36, 25, 36, 25, 25, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 50, 50, 50, 50, 25, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850325 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 Building ZINC001285850325 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850325 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 753) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850325 none CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 48, 50, 38, 27, 38, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 48, 48, 50, 50, 50, 50, 27, 27, 27, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 754) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1) `ZINC001285850325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285850325 none CNC(=O)C1(C(=O)N2CC[C@H]2CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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, 45, 50, 36, 25, 36, 25, 25, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 50, 50, 50, 50, 25, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850325 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850325 Building ZINC001285850350 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850350 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/755 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/755' -> `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]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850350 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 17, 22, 22, 27, 30, 30, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 27, 27, 30, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/756 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/756' -> `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]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850350 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 18, 18, 25, 29, 29, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 25, 25, 29, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850350 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 Building ZINC001285850350 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850350 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 755) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850350 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 17, 17, 17, 17, 17, 22, 22, 27, 30, 30, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 17, 17, 17, 27, 27, 30, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 756) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850350 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 18, 18, 25, 29, 29, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 25, 25, 29, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850350 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850350 Building ZINC001285850353 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850353 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/757 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/757' -> `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]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850353 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 18, 18, 26, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 26, 26, 29, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/758 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/758' -> `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]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850353 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 16, 16, 16, 16, 20, 20, 27, 30, 30, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 16, 16, 16, 27, 27, 30, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850353 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 Building ZINC001285850353 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850353 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 757) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850353 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 15, 15, 15, 15, 18, 18, 26, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 26, 26, 29, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 758) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1) `ZINC001285850353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285850353 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN1C(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 16, 16, 16, 16, 20, 20, 27, 30, 30, 30, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 16, 16, 16, 27, 27, 30, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850353 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850353 Building ZINC001285850421 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850421 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/759 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850421 none COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 32, 31, 32, 31, 31, 31, 22, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/760 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850421 none COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 36, 39, 36, 36, 36, 23, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 36, 36, 36, 36, 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, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850421 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 Building ZINC001285850421 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850421 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 759) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850421 none COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 32, 31, 32, 31, 31, 31, 22, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 31, 31, 31, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 760) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850421 none COc1ccnc(O)c1C(=O)N1CC[C@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 36, 39, 36, 36, 36, 23, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 36, 36, 36, 36, 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, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850421 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850421 Building ZINC001285850422 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850422 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/761 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850422 none COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 31, 36, 31, 31, 31, 24, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 31, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/762 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850422 none COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 34, 37, 34, 34, 34, 23, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 34, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850422 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 Building ZINC001285850422 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285850422 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 761) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285850422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285850422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850422 none COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 31, 36, 31, 31, 31, 24, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 31, 31, 31, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 762) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285850422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285850422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001285850422 none COc1ccnc(O)c1C(=O)N1CC[C@@H]1CNC(=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', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 34, 37, 34, 34, 34, 23, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 100, 34, 34, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285850422 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285850422 Building ZINC001285856288 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856288 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/763 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@@H]1CNC(=O)CC1OCCCO1) `ZINC001285856288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856288 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 17, 17, 17, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 17, 46, 46, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/764 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@@H]1CNC(=O)CC1OCCCO1) `ZINC001285856288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856288 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 25, 25, 25, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 25, 48, 48, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856288 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 Building ZINC001285856288 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856288 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 763) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@@H]1CNC(=O)CC1OCCCO1) `ZINC001285856288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856288 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 17, 17, 17, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 17, 46, 46, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 764) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@@H]1CNC(=O)CC1OCCCO1) `ZINC001285856288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856288 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 25, 25, 25, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 25, 48, 48, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856288 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856288 Building ZINC001285856290 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856290 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/765 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001285856290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856290 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 23, 23, 23, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 23, 47, 47, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/766 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001285856290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856290 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 17, 17, 17, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 17, 47, 47, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856290 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 Building ZINC001285856290 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856290 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 765) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001285856290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856290 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 23, 23, 23, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 23, 47, 47, 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 766) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CC1OCCCO1) `ZINC001285856290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285856290 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CC1OCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 17, 17, 17, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 17, 47, 47, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856290 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856290 Building ZINC001285856961 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856961 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/767 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285856961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856961 none Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 24, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/768 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285856961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856961 none Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 15, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856961 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 Building ZINC001285856961 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856961 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 767) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285856961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856961 none Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 24, 24, 24, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 768) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285856961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856961 none Cc1n[nH]c(C)c1CC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 15, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 26, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856961 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856961 Building ZINC001285856962 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856962 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/769 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285856962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856962 none Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 16, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 29, 16, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/770 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285856962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856962 none Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 27, 27, 27, 12, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856962 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 Building ZINC001285856962 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285856962 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 769) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285856962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285856962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856962 none Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 16, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 29, 16, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 770) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285856962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285856962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001285856962 none Cc1n[nH]c(C)c1CC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 27, 27, 27, 12, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285856962 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285856962 Building ZINC001285862159 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862159 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/771 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862159 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 43, 43, 49, 50, 50, 50, 50, 50, 27, 27, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 49, 49, 50, 50, 27, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/772 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862159 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 50, 50, 50, 26, 26, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 45, 45, 49, 49, 50, 50, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862159 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 Building ZINC001285862159 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862159 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 771) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862159 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 43, 43, 49, 50, 50, 50, 50, 50, 27, 27, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 49, 49, 50, 50, 27, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 772) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862159 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 50, 50, 50, 26, 26, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 45, 45, 49, 49, 50, 50, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862159 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862159 Building ZINC001285862160 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862160 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/773 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862160 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 46, 46, 49, 50, 50, 50, 50, 50, 27, 27, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 49, 49, 50, 50, 27, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/774 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862160 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 43, 43, 49, 50, 50, 50, 50, 50, 26, 26, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 49, 49, 50, 50, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862160 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 Building ZINC001285862160 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862160 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 773) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862160 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 46, 46, 49, 50, 50, 50, 50, 50, 27, 27, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 49, 49, 50, 50, 27, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 774) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862160 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 43, 43, 49, 50, 50, 50, 50, 50, 26, 26, 14, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 49, 49, 50, 50, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862160 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862160 Building ZINC001285862161 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862161 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/775 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862161 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 48, 48, 49, 50, 50, 50, 50, 50, 27, 27, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 49, 49, 50, 50, 27, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/776 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862161 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 46, 46, 48, 50, 50, 50, 50, 50, 26, 26, 15, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 48, 48, 50, 50, 26, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862161 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 Building ZINC001285862161 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862161 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 775) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862161 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 48, 48, 49, 50, 50, 50, 50, 50, 27, 27, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 49, 49, 50, 50, 27, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 776) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862161 none C[C@@H](Cc1cnc[nH]1)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 46, 46, 48, 50, 50, 50, 50, 50, 26, 26, 15, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 48, 48, 50, 50, 26, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862161 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862161 Building ZINC001285862162 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862162 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/777 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862162 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 46, 46, 48, 50, 50, 50, 50, 50, 25, 25, 14, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 48, 48, 50, 50, 25, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/778 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862162 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 48, 48, 49, 50, 50, 50, 50, 50, 27, 27, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 49, 49, 50, 50, 27, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862162 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 Building ZINC001285862162 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285862162 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 777) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285862162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285862162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862162 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 46, 46, 48, 50, 50, 50, 50, 50, 25, 25, 14, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 46, 46, 48, 48, 50, 50, 25, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 778) grep: /scratch/xiaobo/3016/xbk-8058097.37/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](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285862162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285862162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001285862162 none C[C@H](Cc1cnc[nH]1)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 48, 48, 49, 50, 50, 50, 50, 50, 27, 27, 13, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 49, 49, 50, 50, 27, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285862162 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285862162 Building ZINC001285863533 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285863533 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/779 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285863533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863533 none Cn1cc(CCC(=O)NC[C@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 18, 18, 18, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 18, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/780 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285863533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863533 none Cn1cc(CCC(=O)NC[C@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 14, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285863533 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 Building ZINC001285863533 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285863533 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 779) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285863533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863533 none Cn1cc(CCC(=O)NC[C@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 18, 18, 18, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 18, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 780) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285863533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863533 none Cn1cc(CCC(=O)NC[C@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 14, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285863533 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863533 Building ZINC001285863535 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285863535 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/781 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285863535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863535 none Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 14, 14, 14, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 14, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/782 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285863535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863535 none Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285863535 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 Building ZINC001285863535 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285863535 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 781) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285863535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863535 none Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 14, 14, 14, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 14, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 782) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001285863535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285863535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285863535 none Cn1cc(CCC(=O)NC[C@@H]2CCN2C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285863535 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285863535 Building ZINC001285866813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285866813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/783 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1) `ZINC001285866813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285866813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866813 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 11, 11, 11, 38, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 11, 38, 38, 44, 44, 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/784 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1) `ZINC001285866813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285866813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866813 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 19, 19, 19, 44, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 19, 44, 44, 48, 48, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285866813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 Building ZINC001285866813 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285866813 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 783) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1) `ZINC001285866813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285866813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866813 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 11, 11, 11, 38, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 11, 38, 38, 44, 44, 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 784) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1) `ZINC001285866813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285866813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866813 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 19, 19, 19, 44, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 19, 44, 44, 48, 48, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285866813 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866813 Building ZINC001285866814 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285866814 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/785 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CCc1ccncn1) `ZINC001285866814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285866814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 18, 18, 18, 43, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 18, 43, 43, 47, 47, 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: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/786 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CCc1ccncn1) `ZINC001285866814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285866814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 11, 11, 11, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 11, 37, 37, 44, 44, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285866814 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 Building ZINC001285866814 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285866814 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 785) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CCc1ccncn1) `ZINC001285866814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285866814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 18, 18, 18, 43, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 18, 43, 43, 47, 47, 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: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 786) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC[C@H]1CNC(=O)CCc1ccncn1) `ZINC001285866814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285866814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285866814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCc1ccncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 11, 11, 11, 37, 44, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 11, 37, 37, 44, 44, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285866814 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285866814 Building ZINC001285867255 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285867255 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/787 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1) `ZINC001285867255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285867255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867255 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 13, 35, 32, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 13, 35, 35, 44, 44, 46, 46, 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: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/788 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1) `ZINC001285867255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285867255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867255 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 5, 10, 20, 20, 20, 41, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 20, 41, 41, 47, 47, 49, 47, 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: 289 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285867255 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 Building ZINC001285867255 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285867255 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 787) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1) `ZINC001285867255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285867255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867255 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 13, 35, 32, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 13, 35, 35, 44, 44, 46, 46, 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: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 788) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1) `ZINC001285867255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285867255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867255 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 5, 10, 20, 20, 20, 41, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 20, 41, 41, 47, 47, 49, 47, 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: 289 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285867255 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867255 Building ZINC001285867256 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285867256 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/789 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1) `ZINC001285867256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285867256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 5, 10, 17, 17, 17, 42, 34, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 17, 42, 42, 46, 46, 45, 47, 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: 284 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/790 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1) `ZINC001285867256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285867256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 13, 35, 32, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 13, 35, 35, 44, 44, 46, 46, 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: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285867256 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 Building ZINC001285867256 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285867256 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 789) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1) `ZINC001285867256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285867256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 5, 10, 17, 17, 17, 42, 34, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 17, 42, 42, 46, 46, 45, 47, 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: 284 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 790) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1) `ZINC001285867256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285867256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285867256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 13, 13, 13, 35, 32, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 13, 35, 35, 44, 44, 46, 46, 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: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285867256 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285867256 Building ZINC001285873721 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285873721 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/791 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285873721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285873721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873721 none COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 29, 21, 21, 13, 13, 13, 10, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 13, 10, 10, 5, 5, 5, 5, 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/792 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285873721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285873721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873721 none COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 33, 29, 29, 16, 16, 16, 13, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 29, 29, 29, 29, 16, 13, 13, 7, 7, 7, 7, 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: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285873721 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 Building ZINC001285873721 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285873721 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 791) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285873721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285873721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873721 none COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 29, 21, 21, 13, 13, 13, 10, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 13, 10, 10, 5, 5, 5, 5, 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 792) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285873721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285873721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873721 none COCCOCCC(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 33, 29, 29, 16, 16, 16, 13, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 29, 29, 29, 29, 16, 13, 13, 7, 7, 7, 7, 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: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285873721 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873721 Building ZINC001285873725 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285873725 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/793 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285873725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285873725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873725 none COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 33, 27, 27, 15, 15, 15, 13, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 27, 27, 27, 27, 15, 13, 13, 7, 7, 7, 7, 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: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/794 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285873725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285873725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873725 none COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 27, 18, 18, 11, 11, 11, 9, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 18, 18, 18, 18, 11, 9, 9, 5, 5, 5, 5, 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285873725 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 Building ZINC001285873725 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285873725 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 793) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285873725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285873725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873725 none COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 33, 27, 27, 15, 15, 15, 13, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 46, 46, 27, 27, 27, 27, 15, 13, 13, 7, 7, 7, 7, 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: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 794) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285873725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285873725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285873725 none COCCOCCC(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 27, 18, 18, 11, 11, 11, 9, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 18, 18, 18, 18, 11, 9, 9, 5, 5, 5, 5, 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285873725 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285873725 Building ZINC001285875004 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285875004 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/795 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285875004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 22, 22, 27, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 10, 22, 22, 27, 27, 27, 27, 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/796 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285875004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 6, 11, 11, 11, 28, 19, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 11, 28, 28, 28, 28, 28, 28, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285875004 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 Building ZINC001285875004 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285875004 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 795) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285875004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 22, 22, 27, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 10, 22, 22, 27, 27, 27, 27, 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 796) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285875004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 6, 11, 11, 11, 28, 19, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 11, 28, 28, 28, 28, 28, 28, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285875004 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875004 Building ZINC001285875006 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285875006 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/797 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285875006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875006 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 6, 11, 11, 11, 28, 20, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 11, 28, 28, 28, 28, 28, 28, 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/798 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285875006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875006 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 23, 22, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 10, 23, 23, 28, 28, 28, 28, 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285875006 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 Building ZINC001285875006 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285875006 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 797) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285875006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875006 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 6, 11, 11, 11, 28, 20, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 6, 11, 28, 28, 28, 28, 28, 28, 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 798) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1) `ZINC001285875006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285875006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285875006 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1CNC(=O)CCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 23, 22, 28, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 10, 23, 23, 28, 28, 28, 28, 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285875006 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285875006 Building ZINC001285881259 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285881259 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/799 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285881259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881259 none Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 15, 15, 15, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 15, 7, 7, 4, 4, 4, 4, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/800 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285881259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881259 none Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 17, 8, 8, 4, 4, 4, 4, 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285881259 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 Building ZINC001285881259 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285881259 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 799) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285881259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881259 none Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 15, 15, 15, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 15, 7, 7, 4, 4, 4, 4, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 800) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285881259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881259 none Cc1noc(CCC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 17, 8, 8, 4, 4, 4, 4, 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285881259 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881259 Building ZINC001285881260 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285881260 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/801 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285881260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881260 none Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 41, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 41, 41, 17, 8, 8, 4, 4, 4, 4, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/802 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285881260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881260 none Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 15, 15, 15, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 15, 7, 7, 4, 4, 4, 4, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285881260 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 Building ZINC001285881260 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285881260 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 801) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285881260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881260 none Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 41, 17, 17, 17, 8, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 41, 41, 17, 8, 8, 4, 4, 4, 4, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 802) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001285881260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285881260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285881260 none Cc1noc(CCC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 39, 15, 15, 15, 7, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 42, 42, 39, 39, 15, 7, 7, 4, 4, 4, 4, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285881260 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285881260 Building ZINC001285889727 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285889727 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/803 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285889727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889727 none COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 14, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/804 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285889727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889727 none COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285889727 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 Building ZINC001285889727 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285889727 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 803) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285889727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889727 none COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 14, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 804) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285889727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889727 none COc1ccc(CC(=O)NC[C@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285889727 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889727 Building ZINC001285889728 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285889728 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/805 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285889728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889728 none COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/806 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285889728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889728 none COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 13, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285889728 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 Building ZINC001285889728 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285889728 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 805) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285889728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889728 none COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 806) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001285889728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285889728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285889728 none COc1ccc(CC(=O)NC[C@@H]2CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 13, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285889728 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285889728 Building ZINC001285904351 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904351 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/807 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904351 none CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 44, 28, 44, 44, 50, 50, 50, 28, 28, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 5, 5, 5, 5, 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: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/808 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904351 none CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 23, 45, 45, 50, 50, 50, 23, 23, 12, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 6, 6, 6, 6, 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: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904351 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 Building ZINC001285904351 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904351 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 807) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904351 none CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 44, 28, 44, 44, 50, 50, 50, 28, 28, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 5, 5, 5, 5, 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: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 808) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904351 none CC[C@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 23, 45, 45, 50, 50, 50, 23, 23, 12, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 6, 6, 6, 6, 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: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904351 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904351 Building ZINC001285904352 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904352 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/809 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904352 none CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 23, 45, 45, 50, 50, 50, 23, 23, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 5, 5, 5, 5, 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: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/810 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904352 none CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 44, 28, 44, 44, 50, 50, 50, 28, 28, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 5, 5, 5, 5, 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: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904352 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 Building ZINC001285904352 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904352 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 809) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904352 none CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 23, 45, 45, 50, 50, 50, 23, 23, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 5, 5, 5, 5, 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: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 810) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904352 none CC[C@@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 44, 28, 44, 44, 50, 50, 50, 28, 28, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 5, 5, 5, 5, 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: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904352 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904352 Building ZINC001285904353 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904353 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/811 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904353 none CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 47, 30, 47, 47, 50, 50, 50, 30, 30, 16, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 16, 16, 5, 5, 5, 5, 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: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/812 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904353 none CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 50, 28, 50, 50, 50, 50, 50, 28, 28, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 5, 5, 5, 5, 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: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904353 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 Building ZINC001285904353 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904353 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 811) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904353 none CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 47, 30, 47, 47, 50, 50, 50, 30, 30, 16, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 16, 16, 5, 5, 5, 5, 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: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 812) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904353 none CC[C@H](NC(C)=O)C(=O)NC[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 50, 28, 50, 50, 50, 50, 50, 28, 28, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 5, 5, 5, 5, 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: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904353 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904353 Building ZINC001285904354 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904354 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/813 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904354 none CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 48, 25, 48, 48, 50, 50, 50, 25, 25, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 11, 11, 5, 5, 5, 5, 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: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/814 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904354 none CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 47, 30, 47, 47, 50, 50, 50, 30, 30, 17, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 5, 5, 5, 5, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904354 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 Building ZINC001285904354 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285904354 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 813) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285904354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285904354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904354 none CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 48, 25, 48, 48, 50, 50, 50, 25, 25, 11, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 11, 11, 5, 5, 5, 5, 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: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 814) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285904354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285904354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285904354 none CC[C@@H](NC(C)=O)C(=O)NC[C@H]1CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 47, 30, 47, 47, 50, 50, 50, 30, 30, 17, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 5, 5, 5, 5, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285904354 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285904354 Building ZINC001285905290 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285905290 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/815 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001285905290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285905290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285905290 none Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 26, 26, 26, 21, 21, 21, 37, 40, 21, 4, 1, 8, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 40, 40, 26, 37, 37, 40, 40, 120, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 298 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/816 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001285905290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285905290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285905290 none Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 25, 25, 25, 21, 21, 21, 38, 43, 21, 4, 1, 8, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 39, 39, 39, 25, 38, 38, 43, 43, 129, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 315 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285905290 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 Building ZINC001285905290 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285905290 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 815) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001285905290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285905290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285905290 none Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 26, 26, 26, 21, 21, 21, 37, 40, 21, 4, 1, 8, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 40, 40, 26, 37, 37, 40, 40, 120, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 298 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 816) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001285905290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285905290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285905290 none Cc1ccc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 12, 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, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 25, 25, 25, 21, 21, 21, 38, 43, 21, 4, 1, 8, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 39, 39, 39, 25, 38, 38, 43, 43, 129, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 315 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285905290 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285905290 Building ZINC001285912885 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285912885 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/817 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285912885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285912885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285912885 none Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 9, 43, 43, 9, 9, 9, 8, 8, 8, 14, 18, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 43, 43, 43, 15, 43, 9, 14, 14, 18, 18, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 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: 243 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/818 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285912885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285912885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285912885 none Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 9, 42, 42, 9, 9, 9, 7, 7, 7, 16, 21, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 9, 42, 9, 16, 16, 21, 21, 63, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 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: 253 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285912885 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 Building ZINC001285912885 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285912885 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 817) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285912885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285912885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285912885 none Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 9, 43, 43, 9, 9, 9, 8, 8, 8, 14, 18, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 43, 43, 43, 15, 43, 9, 14, 14, 18, 18, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 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: 243 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 818) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285912885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285912885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285912885 none Cc1ncncc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 9, 42, 42, 9, 9, 9, 7, 7, 7, 16, 21, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 9, 42, 9, 16, 16, 21, 21, 63, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 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: 253 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285912885 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285912885 Building ZINC001285914799 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914799 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/819 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cncc3nc[nH]c32)CC1) `ZINC001285914799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cncc3nc[nH]c32)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', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/820 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cncc3nc[nH]c32)CC1) `ZINC001285914799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cncc3nc[nH]c32)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', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 12, 29, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 30, 50, 50, 50, 29, 29, 29, 29] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914799 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 Building ZINC001285914799 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914799 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 819) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cncc3nc[nH]c32)CC1) `ZINC001285914799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cncc3nc[nH]c32)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', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 820) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cncc3nc[nH]c32)CC1) `ZINC001285914799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cncc3nc[nH]c32)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', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 12, 29, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 30, 50, 50, 50, 29, 29, 29, 29] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914799 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914799 Building ZINC001285914827 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914827 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/821 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285914827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285914827 none CC(=O)NC(C)(C)C(=O)NC1(CNC(=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.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, 1, 11, 8, 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, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/822 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285914827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285914827 none CC(=O)NC(C)(C)C(=O)NC1(CNC(=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.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, 1, 11, 8, 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, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914827 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 Building ZINC001285914827 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914827 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 821) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NC(C)(C)C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285914827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285914827 none CC(=O)NC(C)(C)C(=O)NC1(CNC(=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.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, 1, 11, 8, 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, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 822) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)NC(C)(C)C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285914827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285914827 none CC(=O)NC(C)(C)C(=O)NC1(CNC(=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.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, 1, 11, 8, 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, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 19, 19, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914827 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914827 Building ZINC001285914830 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914830 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/823 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914830 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 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: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/824 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914830 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914830 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 Building ZINC001285914830 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914830 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 823) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914830 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 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: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 824) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914830 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914830 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914830 Building ZINC001285914831 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914831 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/825 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914831 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/826 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914831 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914831 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 Building ZINC001285914831 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914831 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 825) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914831 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 826) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)CC1) `ZINC001285914831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914831 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3n[nH]cc3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914831 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914831 Building ZINC001285914833 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914833 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/827 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914833 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 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: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/828 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914833 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914833 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 Building ZINC001285914833 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914833 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 827) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914833 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 24, 24, 24, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24] 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: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 828) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914833 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 25, 25, 25, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914833 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914833 Building ZINC001285914834 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914834 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/829 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914834 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/830 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914834 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 26, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914834 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 Building ZINC001285914834 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285914834 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 829) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285914834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914834 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 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: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 830) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)CC1) `ZINC001285914834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285914834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285914834 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nc[nH]c3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 26, 26, 26, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 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, 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/3016/xbk-8058097.37/working/building/ZINC001285914834 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285914834 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285914834 Building ZINC001285915265 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915265 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/831 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285915265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285915265 none Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 6, 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, 23, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/832 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285915265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285915265 none Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 6, 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, 23, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915265 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 Building ZINC001285915265 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915265 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 831) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285915265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285915265 none Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 6, 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, 23, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 832) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285915265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285915265 none Cn1c(=O)cccc1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 6, 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, 23, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915265 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915265 Building ZINC001285915382 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915382 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/833 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cccn3nnnc23)CC1) `ZINC001285915382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915382 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cccn3nnnc23)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 50, 50, 50, 33, 33, 33, 33] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/834 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cccn3nnnc23)CC1) `ZINC001285915382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915382 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cccn3nnnc23)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 50, 50, 50, 33, 33, 33, 33] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915382 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 Building ZINC001285915382 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915382 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 833) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cccn3nnnc23)CC1) `ZINC001285915382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915382 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cccn3nnnc23)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 50, 50, 50, 33, 33, 33, 33] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 834) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cccn3nnnc23)CC1) `ZINC001285915382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915382 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cccn3nnnc23)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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 50, 50, 50, 33, 33, 33, 33] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915382 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915382 Building ZINC001285915860 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915860 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/835 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1) `ZINC001285915860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915860 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 8, 8, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 13, 13, 32, 36, 40, 47, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 32, 32, 40, 40, 40, 40, 47, 47, 50, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/836 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1) `ZINC001285915860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915860 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 8, 8, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 13, 13, 32, 36, 40, 47, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 32, 32, 40, 40, 40, 40, 47, 47, 50, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915860 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 Building ZINC001285915860 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285915860 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 835) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1) `ZINC001285915860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285915860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915860 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 8, 8, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 13, 13, 32, 36, 40, 47, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 32, 32, 40, 40, 40, 40, 47, 47, 50, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 836) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1) `ZINC001285915860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285915860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285915860 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)CCCCc2cnn[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 8, 8, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 13, 13, 32, 36, 40, 47, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 32, 32, 40, 40, 40, 40, 47, 47, 50, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285915860 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285915860 Building ZINC001285916258 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916258 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/837 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916258 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 1, 11, 8, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 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, 35, 43, 10, 10, 10, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 35, 35, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/838 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916258 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 1, 11, 8, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 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, 35, 41, 12, 12, 12, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 35, 35, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916258 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 Building ZINC001285916258 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916258 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 837) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N(C)CC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916258 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 1, 11, 8, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 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, 35, 43, 10, 10, 10, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 35, 35, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 838) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N(C)CC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916258 none CC(C)C(=O)N(C)CC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 1, 11, 8, 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, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 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, 35, 41, 12, 12, 12, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 35, 35, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916258 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916258 Building ZINC001285916320 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916320 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/839 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285916320 none CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 47, 50, 47, 47, 47, 47, 24, 47, 21, 21, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 47, 47, 47, 47, 47, 47, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/840 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285916320 none CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 48, 50, 48, 48, 48, 48, 31, 48, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 48, 48, 48, 48, 48, 48, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916320 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 Building ZINC001285916320 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916320 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 839) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285916320 none CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 47, 50, 47, 47, 47, 47, 24, 47, 21, 21, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50, 47, 47, 47, 47, 47, 47, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 840) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(=O)N1CCC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285916320 none CC(=O)N1CCC[C@H]1C(=O)NC1(CNC(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 48, 50, 48, 48, 48, 48, 31, 48, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 48, 48, 48, 48, 48, 48, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916320 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916320 Building ZINC001285916360 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916360 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/841 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2nc3ncccn3n2)CC1) `ZINC001285916360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916360 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2nc3ncccn3n2)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.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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'] 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, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/842 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2nc3ncccn3n2)CC1) `ZINC001285916360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916360 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2nc3ncccn3n2)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.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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'] 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, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916360 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 Building ZINC001285916360 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916360 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 841) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2nc3ncccn3n2)CC1) `ZINC001285916360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916360 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2nc3ncccn3n2)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.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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'] 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, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 842) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2nc3ncccn3n2)CC1) `ZINC001285916360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916360 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2nc3ncccn3n2)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.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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'] 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, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916360 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916360 Building ZINC001285916365 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285916365 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/843 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/844 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/845 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/845' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/846 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/846' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916365 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 Building ZINC001285916365 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285916365 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 843) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 844) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 845) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 846) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916365 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 Building ZINC001285916365 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285916365 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 843) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 844) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 845) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 846) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916365 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 Building ZINC001285916365 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285916365 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 843) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 844) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 845) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 32, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 846) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)CC1) `ZINC001285916365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285916365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285916365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)C23CCCN2CCC3)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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 30, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916365 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916365 Building ZINC001285916786 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916786 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/847 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CCC(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285916786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285916786 none Cn1ccc(CCC(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 46, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 49, 49, 46, 46, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/848 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CCC(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285916786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285916786 none Cn1ccc(CCC(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 48, 48, 45, 45, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916786 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 Building ZINC001285916786 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916786 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 847) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CCC(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285916786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285916786 none Cn1ccc(CCC(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 46, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 49, 49, 46, 46, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 848) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(CCC(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285916786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285916786 none Cn1ccc(CCC(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 48, 48, 45, 45, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916786 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916786 Building ZINC001285916869 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916869 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/849 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916869 none Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 50, 50, 50, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 100, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/850 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916869 none Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 26, 26, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 100, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916869 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 Building ZINC001285916869 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285916869 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 849) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285916869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916869 none Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 50, 50, 50, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 100, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 850) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285916869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285916869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285916869 none Cc1ncnc(O)c1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 26, 26, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 100, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285916869 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285916869 Building ZINC001285917189 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917189 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/851 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)CC1) `ZINC001285917189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917189 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 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, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/852 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)CC1) `ZINC001285917189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917189 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917189 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 Building ZINC001285917189 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917189 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 851) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)CC1) `ZINC001285917189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917189 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 20, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 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, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 852) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)CC1) `ZINC001285917189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917189 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 18, 18, 18, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917189 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917189 Building ZINC001285917191 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917191 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/853 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)CC1) `ZINC001285917191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917191 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/854 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)CC1) `ZINC001285917191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917191 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917191 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 Building ZINC001285917191 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917191 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 853) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)CC1) `ZINC001285917191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917191 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 854) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)CC1) `ZINC001285917191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917191 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)[C@H]2CCc3nccn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 1, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 19, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917191 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917191 Building ZINC001285917200 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917200 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/855 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917200 none CC(C)[C@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 45, 30, 46, 30, 30, 30, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 30, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 261 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/856 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917200 none CC(C)[C@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 42, 30, 47, 30, 30, 30, 17, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 30, 30, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917200 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 Building ZINC001285917200 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917200 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 855) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917200 none CC(C)[C@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 45, 30, 46, 30, 30, 30, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 30, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 261 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 856) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917200 none CC(C)[C@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 42, 30, 47, 30, 30, 30, 17, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 30, 30, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917200 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917200 Building ZINC001285917202 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917202 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/857 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917202 none CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 30, 46, 30, 30, 30, 16, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 30, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 287 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/858 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917202 none CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 50, 31, 47, 31, 31, 31, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 31, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 244 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917202 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 Building ZINC001285917202 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917202 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 857) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917202 none CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 50, 30, 46, 30, 30, 30, 16, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 30, 30, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 16, 16, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 287 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 858) grep: /scratch/xiaobo/3016/xbk-8058097.37/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@@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)N(C)C) `ZINC001285917202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001285917202 none CC(C)[C@@H](C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 50, 31, 47, 31, 31, 31, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 31, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 244 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917202 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917202 Building ZINC001285917235 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917235 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/859 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285917235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285917235 none COc1nccc(C(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/860 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285917235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285917235 none COc1nccc(C(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917235 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 Building ZINC001285917235 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917235 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 859) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nccc(C(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285917235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285917235 none COc1nccc(C(=O)NC2(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 860) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nccc(C(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285917235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285917235 none COc1nccc(C(=O)NC2(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917235 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917235 Building ZINC001285917248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/861 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/862 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/863 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/863' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/864 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/864' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 Building ZINC001285917248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 861) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 862) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 863) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 864) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 Building ZINC001285917248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 861) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 862) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 863) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 864) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 Building ZINC001285917248 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917248 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 861) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 862) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 31, 50, 27, 27, 27, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 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: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 863) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 864) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917248.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917248 none CCN1CCOC[C@@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 28, 50, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 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: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917248 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917248 Building ZINC001285917249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/865 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/866 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/867 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/867' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/868 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/868' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 Building ZINC001285917249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 865) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 866) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 867) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 868) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 Building ZINC001285917249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 865) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 866) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 867) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 868) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 Building ZINC001285917249 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285917249 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 865) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 866) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 35, 50, 23, 23, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 151 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 867) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 868) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285917249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285917249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285917249 none CCN1CCOC[C@H]1C(=O)NC1(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 50, 50, 50, 50, 36, 50, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 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: 157 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917249 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917249 Building ZINC001285917261 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917261 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/869 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2ccc(C(N)=O)nc2)CC1) `ZINC001285917261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917261 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2ccc(C(N)=O)nc2)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', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/870 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2ccc(C(N)=O)nc2)CC1) `ZINC001285917261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917261 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2ccc(C(N)=O)nc2)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', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917261 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 Building ZINC001285917261 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917261 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 869) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2ccc(C(N)=O)nc2)CC1) `ZINC001285917261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917261 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2ccc(C(N)=O)nc2)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', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 870) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2ccc(C(N)=O)nc2)CC1) `ZINC001285917261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917261 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2ccc(C(N)=O)nc2)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', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 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, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917261 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917261 Building ZINC001285917283 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917283 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/871 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cnn3cccnc23)CC1) `ZINC001285917283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917283 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cnn3cccnc23)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.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 50, 50, 37, 37, 37, 37] 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/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/872 `/scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cnn3cccnc23)CC1) `ZINC001285917283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917283 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cnn3cccnc23)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.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 50, 50, 37, 37, 37, 37] 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/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917283 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 Building ZINC001285917283 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285917283 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 871) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cnn3cccnc23)CC1) `ZINC001285917283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285917283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917283 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cnn3cccnc23)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.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 50, 50, 37, 37, 37, 37] 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/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 872) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NCC1(NC(=O)c2cnn3cccnc23)CC1) `ZINC001285917283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285917283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285917283 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)c2cnn3cccnc23)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.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 50, 50, 37, 37, 37, 37] 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/3016/xbk-8058097.37/working/building/ZINC001285917283 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285917283 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285917283 Building ZINC001285918861 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285918861 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/873 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/874 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/875 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/875' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/876 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/876' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285918861 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 Building ZINC001285918861 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285918861 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 873) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 874) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 875) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 876) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285918861 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 Building ZINC001285918861 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285918861 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 873) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 874) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 875) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 876) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285918861 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 Building ZINC001285918861 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001285918861 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 873) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 874) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 40, 30, 40, 8, 5, 8, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 45, 45, 40, 40, 40, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `2' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 2 (index: 875) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `3' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 3 (index: 876) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285918861.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001285918861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285918861 none CCCN(C)CC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 36, 27, 36, 6, 4, 6, 4, 4, 4, 4, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 42, 42, 36, 36, 36, 27, 27, 4, 4, 4, 4, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285918861 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 3: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/3.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/1.* 2: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/2.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285918861 Building ZINC001285919130 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919130 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/877 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285919130 none CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 30, 9, 5, 9, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/878 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285919130 none CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 25, 5, 3, 5, 3, 3, 3, 3, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 25, 25, 3, 3, 3, 3, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919130 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 Building ZINC001285919130 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919130 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 877) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)SCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285919130 none CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 30, 9, 5, 9, 5, 5, 4, 5, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 30, 30, 5, 5, 8, 8, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 203 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 878) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)SCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285919130 none CC(C)SCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 25, 5, 3, 5, 3, 3, 3, 3, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 25, 25, 3, 3, 3, 3, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919130 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919130 Building ZINC001285919299 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919299 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/879 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285919299 none CSCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 8, 4, 8, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 29, 29, 29, 29, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/880 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285919299 none CSCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 11, 6, 11, 6, 6, 4, 6, 9, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 28, 28, 28, 28, 6, 6, 9, 9, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 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]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919299 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 Building ZINC001285919299 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919299 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 879) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CSCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285919299 none CSCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 8, 4, 8, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 29, 29, 29, 29, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 880) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CSCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285919299 none CSCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 11, 6, 11, 6, 6, 4, 6, 9, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 28, 28, 28, 28, 6, 6, 9, 9, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 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]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919299 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919299 Building ZINC001285919700 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919700 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/881 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1) `ZINC001285919700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919700 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 17, 19, 6, 6, 6, 23, 23, 45, 45, 45, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 19, 19, 57, 6, 6, 45, 45, 6, 6] 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, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/882 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1) `ZINC001285919700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919700 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 17, 20, 12, 12, 12, 27, 27, 49, 49, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 20, 20, 60, 12, 12, 49, 49, 12, 12] 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, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919700 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 Building ZINC001285919700 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919700 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 881) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1) `ZINC001285919700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919700 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 17, 19, 6, 6, 6, 23, 23, 45, 45, 45, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 19, 19, 57, 6, 6, 45, 45, 6, 6] 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, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 882) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1) `ZINC001285919700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919700 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 8, 1, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 17, 20, 12, 12, 12, 27, 27, 49, 49, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 20, 20, 60, 12, 12, 49, 49, 12, 12] 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, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919700 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919700 Building ZINC001285919712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/883 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1) `ZINC001285919712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919712 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 10, 16, 6, 6, 6, 20, 20, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 48, 6, 6, 46, 46, 6, 6] 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, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/884 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1) `ZINC001285919712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919712 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 10, 13, 8, 8, 8, 21, 21, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 39, 8, 8, 50, 50, 8, 8] 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, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 Building ZINC001285919712 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919712 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 883) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1) `ZINC001285919712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919712 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 10, 16, 6, 6, 6, 20, 20, 46, 46, 46, 46, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 48, 6, 6, 46, 46, 6, 6] 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, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 884) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1) `ZINC001285919712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285919712 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cncs2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 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, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 10, 13, 8, 8, 8, 21, 21, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 39, 8, 8, 50, 50, 8, 8] 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, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919712 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919712 Building ZINC001285919738 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919738 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/885 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919738 none CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 46, 30, 12, 30, 30, 35, 6, 12, 6, 6, 4, 6, 9, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 48, 48, 48, 48, 48, 46, 46, 35, 35, 35, 6, 6, 9, 9, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 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: 303 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/886 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919738 none CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 46, 25, 9, 25, 25, 32, 4, 9, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 47, 47, 47, 47, 47, 46, 46, 32, 32, 32, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 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: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919738 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 Building ZINC001285919738 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919738 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 885) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919738 none CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 46, 30, 12, 30, 30, 35, 6, 12, 6, 6, 4, 6, 9, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 48, 48, 48, 48, 48, 46, 46, 35, 35, 35, 6, 6, 9, 9, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 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: 303 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 886) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919738 none CCC[C@@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 46, 25, 9, 25, 25, 32, 4, 9, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 47, 47, 47, 47, 47, 46, 46, 32, 32, 32, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 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: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919738 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919738 Building ZINC001285919739 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919739 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/887 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919739 none CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 44, 29, 14, 29, 29, 32, 6, 14, 6, 6, 4, 6, 9, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 47, 47, 47, 47, 47, 44, 44, 32, 32, 32, 6, 6, 9, 9, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 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: 282 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/888 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919739 none CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 45, 24, 10, 24, 24, 28, 4, 10, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 47, 47, 47, 47, 47, 45, 45, 28, 28, 28, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 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: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919739 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 Building ZINC001285919739 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285919739 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 887) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285919739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919739 none CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 44, 29, 14, 29, 29, 32, 6, 14, 6, 6, 4, 6, 9, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 47, 47, 47, 47, 47, 44, 44, 32, 32, 32, 6, 6, 9, 9, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 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: 282 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 888) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285919739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285919739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285919739 none CCC[C@H](OC)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 45, 24, 10, 24, 24, 28, 4, 10, 4, 4, 4, 4, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 47, 47, 47, 47, 47, 45, 45, 28, 28, 28, 4, 4, 4, 4, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 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: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285919739 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285919739 Building ZINC001285920261 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920261 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/889 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285920261 none COCCCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 33, 32, 27, 7, 4, 7, 4, 4, 4, 4, 5, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 49, 33, 33, 33, 33, 27, 27, 4, 4, 5, 5, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/890 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285920261 none COCCCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 32, 30, 10, 6, 10, 6, 6, 4, 6, 7, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 33, 33, 33, 33, 30, 30, 6, 6, 7, 7, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920261 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 Building ZINC001285920261 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920261 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 889) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285920261 none COCCCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 33, 32, 27, 7, 4, 7, 4, 4, 4, 4, 5, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 49, 33, 33, 33, 33, 27, 27, 4, 4, 5, 5, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 890) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COCCCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285920261 none COCCCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 32, 30, 10, 6, 10, 6, 6, 4, 6, 7, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 33, 33, 33, 33, 30, 30, 6, 6, 7, 7, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920261 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920261 Building ZINC001285920269 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920269 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/891 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285920269 none CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 24, 48, 9, 24, 9, 9, 4, 9, 14, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 48, 48, 48, 9, 9, 14, 14, 19, 19, 57, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 269 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/892 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285920269 none CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 20, 46, 4, 20, 4, 4, 4, 4, 10, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 46, 46, 46, 46, 46, 46, 4, 4, 10, 10, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920269 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 Building ZINC001285920269 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920269 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 891) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(F)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285920269 none CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 24, 48, 9, 24, 9, 9, 4, 9, 14, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 48, 48, 48, 9, 9, 14, 14, 19, 19, 57, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 269 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 892) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(F)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285920269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285920269 none CC(C)=C(F)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 20, 46, 4, 20, 4, 4, 4, 4, 10, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 46, 46, 46, 46, 46, 46, 4, 4, 10, 10, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 229 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920269 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920269 Building ZINC001285920270 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920270 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/893 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1) `ZINC001285920270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 5, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 11, 14, 6, 6, 6, 21, 21, 46, 46, 46, 46, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 14, 14, 42, 6, 6, 46, 46, 46, 46, 46, 46, 46, 6, 6] 150 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: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/894 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1) `ZINC001285920270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 5, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 10, 13, 5, 5, 5, 16, 16, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 13, 13, 39, 5, 5, 40, 40, 40, 40, 40, 40, 40, 5, 5] 150 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: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920270 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 Building ZINC001285920270 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920270 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 893) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1) `ZINC001285920270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 5, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 11, 14, 6, 6, 6, 21, 21, 46, 46, 46, 46, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 14, 14, 42, 6, 6, 46, 46, 46, 46, 46, 46, 46, 6, 6] 150 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: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 894) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1) `ZINC001285920270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2=CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 5, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 10, 13, 5, 5, 5, 16, 16, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 13, 13, 39, 5, 5, 40, 40, 40, 40, 40, 40, 40, 5, 5] 150 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: 159 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920270 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920270 Building ZINC001285920287 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920287 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/895 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)CC2)C1) `ZINC001285920287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920287 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)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', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 5, 7, 9, 5, 5, 5, 14, 14, 22, 49, 49, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 27, 5, 5, 49, 22, 22, 22, 22, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 259 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/896 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)CC2)C1) `ZINC001285920287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920287 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)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', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 8, 12, 4, 4, 4, 14, 14, 21, 49, 49, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 4, 4, 49, 21, 21, 21, 21, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920287 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 Building ZINC001285920287 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285920287 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 895) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)CC2)C1) `ZINC001285920287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285920287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920287 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)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', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 5, 7, 9, 5, 5, 5, 14, 14, 22, 49, 49, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 27, 5, 5, 49, 22, 22, 22, 22, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 259 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 896) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)CC2)C1) `ZINC001285920287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285920287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285920287 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)C2(C(F)F)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', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 4, 8, 12, 4, 4, 4, 14, 14, 21, 49, 49, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 4, 4, 49, 21, 21, 21, 21, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285920287 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285920287 Building ZINC001285921306 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921306 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/897 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921306 none CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 42, 47, 23, 42, 42, 10, 23, 10, 10, 5, 10, 15, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 47, 47, 47, 47, 47, 47, 47, 42, 42, 42, 10, 10, 15, 15, 20, 20, 60, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 309 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/898 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921306 none CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 42, 48, 19, 42, 42, 4, 19, 4, 4, 4, 4, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 48, 48, 48, 48, 48, 48, 48, 42, 42, 42, 4, 4, 6, 6, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 260 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921306 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 Building ZINC001285921306 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921306 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 897) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921306 none CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 42, 47, 23, 42, 42, 10, 23, 10, 10, 5, 10, 15, 20, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 47, 47, 47, 47, 47, 47, 47, 42, 42, 42, 10, 10, 15, 15, 20, 20, 60, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 309 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 898) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921306 none CC(C)[C@@H](C)C(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 42, 48, 19, 42, 42, 4, 19, 4, 4, 4, 4, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 48, 48, 48, 48, 48, 48, 48, 42, 42, 42, 4, 4, 6, 6, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 260 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921306 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921306 Building ZINC001285921634 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921634 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/899 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921634 none CN(C)CCCC(=O)N1CC(CCO)(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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 26, 24, 5, 3, 5, 3, 3, 3, 3, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 45, 46, 30, 30, 24, 24, 3, 3, 3, 3, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/900 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921634 none CN(C)CCCC(=O)N1CC(CCO)(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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 32, 29, 6, 4, 6, 4, 4, 4, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 46, 46, 38, 38, 29, 29, 4, 4, 5, 5, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921634 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 Building ZINC001285921634 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921634 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 899) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C)CCCC(=O)N1CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921634 none CN(C)CCCC(=O)N1CC(CCO)(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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 26, 24, 5, 3, 5, 3, 3, 3, 3, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 45, 46, 30, 30, 24, 24, 3, 3, 3, 3, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 900) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C)CCCC(=O)N1CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285921634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285921634 none CN(C)CCCC(=O)N1CC(CCO)(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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 32, 29, 6, 4, 6, 4, 4, 4, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 46, 46, 38, 38, 29, 29, 4, 4, 5, 5, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 49, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921634 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921634 Building ZINC001285921684 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921684 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/901 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001285921684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285921684 none Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 9, 17, 9, 9, 4, 9, 15, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 15, 15, 17, 17, 51, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/902 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001285921684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285921684 none Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 14, 6, 14, 6, 6, 4, 6, 8, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 8, 8, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921684 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 Building ZINC001285921684 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921684 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 901) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001285921684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285921684 none Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 9, 17, 9, 9, 4, 9, 15, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 15, 15, 17, 17, 51, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 902) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001285921684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001285921684 none Cc1cc(C)c(C(=O)N2CC(CCO)(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 14, 6, 14, 6, 6, 4, 6, 8, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 8, 8, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921684 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921684 Building ZINC001285921856 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921856 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/903 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1) `ZINC001285921856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285921856 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 12, 16, 6, 6, 6, 21, 21, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 48, 6, 6, 48, 48, 48, 48, 6, 6] 150 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/904 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1) `ZINC001285921856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285921856 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 12, 15, 9, 9, 9, 24, 24, 49, 49, 49, 49, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 45, 9, 9, 49, 49, 49, 49, 9, 9] 150 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: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921856 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 Building ZINC001285921856 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285921856 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 903) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1) `ZINC001285921856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285921856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285921856 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 12, 16, 6, 6, 6, 21, 21, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 48, 6, 6, 48, 48, 48, 48, 6, 6] 150 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 904) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1) `ZINC001285921856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285921856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285921856 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)c2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 12, 15, 9, 9, 9, 24, 24, 49, 49, 49, 49, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 45, 9, 9, 49, 49, 49, 49, 9, 9] 150 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: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285921856 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285921856 Building ZINC001285927234 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927234 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/905 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1) `ZINC001285927234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285927234 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1 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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 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, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 14, 14, 14, 11, 11, 11, 20, 21, 11, 3, 1, 6, 1, 1, 1, 1, 1, 1, 11, 38, 38, 38, 38, 38, 38, 38, 14, 20, 20, 21, 21, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 38] 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]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/906 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1) `ZINC001285927234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285927234 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1 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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 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, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 13, 13, 11, 11, 11, 19, 19, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 13, 19, 19, 19, 19, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35] 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927234 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 Building ZINC001285927234 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927234 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 905) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1) `ZINC001285927234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285927234 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1 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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 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, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 14, 14, 14, 11, 11, 11, 20, 21, 11, 3, 1, 6, 1, 1, 1, 1, 1, 1, 11, 38, 38, 38, 38, 38, 38, 38, 14, 20, 20, 21, 21, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 38] 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]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 906) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1) `ZINC001285927234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285927234 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1 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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 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, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 13, 13, 11, 11, 11, 19, 19, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 13, 19, 19, 19, 19, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35] 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]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927234 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927234 Building ZINC001285927750 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927750 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/907 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927750 none CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 48, 50, 44, 14, 14, 14, 14, 14, 14, 22, 26, 14, 3, 1, 6, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 48, 48, 44, 44, 14, 22, 22, 26, 26, 78, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 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: 382 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/908 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927750 none CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 50, 40, 14, 14, 14, 14, 14, 14, 24, 25, 14, 4, 1, 7, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 14, 24, 24, 25, 25, 75, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 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: 379 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927750 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 Building ZINC001285927750 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927750 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 907) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927750 none CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 48, 50, 44, 14, 14, 14, 14, 14, 14, 22, 26, 14, 3, 1, 6, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 48, 48, 44, 44, 14, 22, 22, 26, 26, 78, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 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: 382 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 908) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927750 none CO[C@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 49, 50, 40, 14, 14, 14, 14, 14, 14, 24, 25, 14, 4, 1, 7, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 45, 45, 40, 40, 14, 24, 24, 25, 25, 75, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 150 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: 379 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927750 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927750 Building ZINC001285927752 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927752 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/909 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927752 none CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 39, 48, 49, 45, 12, 12, 12, 12, 12, 12, 16, 25, 12, 3, 1, 6, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 49, 49, 49, 48, 48, 45, 45, 12, 16, 16, 25, 25, 75, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 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: 383 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/910 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927752 none CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 50, 50, 42, 15, 15, 15, 15, 15, 15, 19, 25, 15, 4, 1, 7, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 45, 45, 42, 42, 15, 19, 19, 25, 25, 75, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 150 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: 382 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927752 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 Building ZINC001285927752 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285927752 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 909) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285927752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927752 none CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 39, 48, 49, 45, 12, 12, 12, 12, 12, 12, 16, 25, 12, 3, 1, 6, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 49, 49, 49, 48, 48, 45, 45, 12, 16, 16, 25, 25, 75, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 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: 383 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 910) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285927752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285927752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001285927752 none CO[C@@H](C)CCC(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 50, 50, 42, 15, 15, 15, 15, 15, 15, 19, 25, 15, 4, 1, 7, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 45, 45, 42, 42, 15, 19, 19, 25, 25, 75, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 150 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: 382 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285927752 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285927752 Building ZINC001285933095 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285933095 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/911 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)CC1) `ZINC001285933095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285933095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285933095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 5, 10, 10, 10, 29, 37, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 10, 29, 29, 37, 37, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/912 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)CC1) `ZINC001285933095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285933095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285933095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 6, 14, 14, 14, 35, 46, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 14, 35, 35, 46, 46, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285933095 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 Building ZINC001285933095 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285933095 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 911) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)CC1) `ZINC001285933095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285933095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285933095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 5, 10, 10, 10, 29, 37, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 10, 29, 29, 37, 37, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 912) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)CC1) `ZINC001285933095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285933095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285933095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)CCc2ccncn2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 6, 14, 14, 14, 35, 46, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 14, 35, 35, 46, 46, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285933095 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285933095 Building ZINC001285938508 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285938508 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/913 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)CC1) `ZINC001285938508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285938508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/914 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)CC1) `ZINC001285938508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285938508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285938508 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 Building ZINC001285938508 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285938508 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 913) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)CC1) `ZINC001285938508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285938508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 19, 19, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 914) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)CC1) `ZINC001285938508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285938508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285938508 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938508 Building ZINC001285938509 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285938509 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/915 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)CC1) `ZINC001285938509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285938509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938509 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 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: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/916 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)CC1) `ZINC001285938509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285938509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938509 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285938509 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 Building ZINC001285938509 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285938509 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 915) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)CC1) `ZINC001285938509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285938509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938509 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 19, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 50, 50, 50, 50, 50, 50, 50, 50, 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: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 916) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)CC1) `ZINC001285938509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285938509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285938509 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)[C@H]2CCc3cncn3C2)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', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 8, 1, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285938509 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285938509 Building ZINC001285942193 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285942193 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/917 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O) `ZINC001285942193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285942193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285942193 none Cn1ccc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.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.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 20, 20, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/918 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O) `ZINC001285942193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285942193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285942193 none Cn1ccc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.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.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 19, 19, 14, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285942193 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 Building ZINC001285942193 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285942193 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 917) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O) `ZINC001285942193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285942193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285942193 none Cn1ccc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.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.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 20, 20, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 918) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1ccc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O) `ZINC001285942193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285942193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001285942193 none Cn1ccc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.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.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 19, 19, 14, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285942193 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285942193 Building ZINC001285943221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285943221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/919 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285943221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285943221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285943221 none Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 22, 22, 22, 8, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/920 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285943221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285943221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285943221 none Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 19, 19, 19, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285943221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 Building ZINC001285943221 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285943221 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 919) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285943221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285943221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285943221 none Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 22, 22, 22, 8, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 920) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001285943221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285943221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285943221 none Cc1cc(C)n(CC(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 19, 19, 19, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285943221 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943221 Building ZINC001285943742 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285943742 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/921 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)COc2cccnc2)CC1) `ZINC001285943742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285943742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285943742 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)COc2cccnc2)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', 'O.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 3, 5, 5, 5, 30, 40, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 5, 30, 30, 50, 50, 50, 50, 2, 2, 2, 2] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/922 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)COc2cccnc2)CC1) `ZINC001285943742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285943742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285943742 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)COc2cccnc2)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', 'O.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 10, 10, 10, 32, 44, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 32, 32, 50, 50, 50, 50, 2, 2, 2, 2] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285943742 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 Building ZINC001285943742 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285943742 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 921) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)COc2cccnc2)CC1) `ZINC001285943742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285943742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285943742 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)COc2cccnc2)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', 'O.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 3, 5, 5, 5, 30, 40, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 5, 30, 30, 50, 50, 50, 50, 2, 2, 2, 2] 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 922) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)COc2cccnc2)CC1) `ZINC001285943742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285943742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285943742 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)COc2cccnc2)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', 'O.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 7, 10, 10, 10, 32, 44, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 32, 32, 50, 50, 50, 50, 2, 2, 2, 2] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285943742 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285943742 Building ZINC001285947186 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285947186 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/923 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC(CCO)(NC(=O)c2cc(F)c[nH]2)C1) `ZINC001285947186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285947186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285947186 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2cc(F)c[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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 17, 17, 17, 32, 40, 17, 20, 20, 20, 41, 41, 41, 41, 41, 41, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 32, 32, 40, 40, 120, 20, 41, 41, 17, 17] 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]) total number of confs: 310 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/924 `/scratch/xiaobo/3016/xbk-8058097.37/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)N1CC(CCO)(NC(=O)c2cc(F)c[nH]2)C1) `ZINC001285947186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285947186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285947186 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2cc(F)c[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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 19, 19, 19, 31, 38, 19, 22, 22, 22, 43, 43, 43, 43, 43, 43, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31, 31, 38, 38, 114, 22, 43, 43, 19, 19] 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]) total number of confs: 293 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285947186 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 Building ZINC001285947186 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285947186 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 923) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC(CCO)(NC(=O)c2cc(F)c[nH]2)C1) `ZINC001285947186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285947186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285947186 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2cc(F)c[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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 17, 17, 17, 32, 40, 17, 20, 20, 20, 41, 41, 41, 41, 41, 41, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 32, 32, 40, 40, 120, 20, 41, 41, 17, 17] 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]) total number of confs: 310 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 924) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)N1CC(CCO)(NC(=O)c2cc(F)c[nH]2)C1) `ZINC001285947186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285947186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285947186 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2cc(F)c[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', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 15, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 19, 19, 19, 31, 38, 19, 22, 22, 22, 43, 43, 43, 43, 43, 43, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31, 31, 38, 38, 114, 22, 43, 43, 19, 19] 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]) total number of confs: 293 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285947186 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285947186 Building ZINC001285950240 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285950240 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/925 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1C) `ZINC001285950240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285950240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285950240 none Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 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, 34, 34, 34, 12, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 100, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/926 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1C) `ZINC001285950240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285950240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285950240 none Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 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, 31, 31, 31, 14, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 100, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285950240 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 Building ZINC001285950240 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285950240 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 925) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1C) `ZINC001285950240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285950240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285950240 none Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 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, 34, 34, 34, 12, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 100, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 926) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1C) `ZINC001285950240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285950240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285950240 none Cc1nnc(O)c(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 3, 3, 7, 4, 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] 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, 31, 31, 31, 14, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 100, 31, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285950240 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285950240 Building ZINC001285951471 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285951471 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/927 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285951471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951471 none CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 24, 50, 21, 21, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/928 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285951471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951471 none CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 26, 50, 23, 23, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285951471 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 Building ZINC001285951471 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285951471 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 927) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285951471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951471 none CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 24, 50, 21, 21, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 928) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285951471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951471 none CN1C(=O)CCC[C@@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 26, 50, 23, 23, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285951471 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951471 Building ZINC001285951472 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285951472 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/929 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285951472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951472 none CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 30, 50, 29, 29, 11, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/930 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285951472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951472 none CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 24, 50, 21, 21, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285951472 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 Building ZINC001285951472 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285951472 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 929) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285951472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951472 none CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 30, 50, 29, 29, 11, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 930) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285951472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285951472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285951472 none CN1C(=O)CCC[C@H]1C(=O)NCC1(NC(=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.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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 24, 50, 21, 21, 10, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285951472 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285951472 Building ZINC001285952354 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285952354 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/931 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)c2nccn3ccnc23)CC1) `ZINC001285952354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285952354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285952354 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)c2nccn3ccnc23)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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 50, 50, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/932 `/scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)c2nccn3ccnc23)CC1) `ZINC001285952354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285952354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285952354 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)c2nccn3ccnc23)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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285952354 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 Building ZINC001285952354 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285952354 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 931) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)c2nccn3ccnc23)CC1) `ZINC001285952354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285952354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285952354 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CNC(=O)c2nccn3ccnc23)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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 50, 50, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 932) grep: /scratch/xiaobo/3016/xbk-8058097.37/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)NC1(CNC(=O)c2nccn3ccnc23)CC1) `ZINC001285952354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285952354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285952354 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CNC(=O)c2nccn3ccnc23)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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (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, 10, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285952354 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285952354 Building ZINC001285953606 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285953606 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/933 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285953606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285953606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285953606 none Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 33, 50, 50, 50, 25, 25, 25, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 100, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 302 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/934 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285953606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285953606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285953606 none Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 37, 50, 50, 50, 28, 28, 28, 13, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 100, 28, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285953606 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 Building ZINC001285953606 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285953606 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 933) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285953606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285953606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285953606 none Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 33, 50, 50, 50, 25, 25, 25, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 100, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 302 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 934) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285953606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285953606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285953606 none Cc1ncnc(O)c1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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, 37, 50, 50, 50, 28, 28, 28, 13, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 100, 28, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 100 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285953606 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285953606 Building ZINC001285957156 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285957156 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/935 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285957156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285957156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285957156 none Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 11, 11, 11, 10, 10, 10, 17, 21, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 40, 11, 17, 17, 21, 21, 63, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/936 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285957156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285957156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285957156 none Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 13, 13, 13, 11, 11, 11, 21, 25, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 43, 43, 13, 21, 21, 25, 25, 75, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285957156 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 Building ZINC001285957156 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285957156 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 935) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285957156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285957156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285957156 none Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 11, 11, 11, 10, 10, 10, 17, 21, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 40, 11, 17, 17, 21, 21, 63, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 936) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001285957156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285957156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001285957156 none Cc1cocc1C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 13, 13, 13, 11, 11, 11, 21, 25, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 43, 43, 13, 21, 21, 25, 25, 75, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285957156 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285957156 Building ZINC001285960548 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285960548 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/937 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001285960548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285960548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285960548 none CCCn1cc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 27, 27, 27, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/938 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001285960548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285960548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285960548 none CCCn1cc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 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, 24, 24, 24, 12, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 30, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285960548 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 Building ZINC001285960548 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285960548 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 937) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCn1cc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001285960548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285960548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285960548 none CCCn1cc(C(=O)NCC2(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 27, 27, 27, 13, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 938) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCCn1cc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1) `ZINC001285960548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285960548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001285960548 none CCCn1cc(C(=O)NCC2(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 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, 24, 24, 24, 12, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 30, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285960548 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285960548 Building ZINC001285964559 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285964559 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/939 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1) `ZINC001285964559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285964559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285964559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 13, 18, 8, 8, 8, 8, 32, 42, 49, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 18, 18, 54, 8, 32, 32, 49, 49, 49, 8, 8] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 353 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/940 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1) `ZINC001285964559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285964559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285964559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 11, 11, 11, 16, 20, 11, 11, 11, 11, 38, 42, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 20, 20, 60, 11, 38, 38, 49, 49, 49, 11, 11] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 346 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285964559 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 Building ZINC001285964559 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285964559 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 939) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1) `ZINC001285964559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285964559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285964559 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 13, 18, 8, 8, 8, 8, 32, 42, 49, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 18, 18, 54, 8, 32, 32, 49, 49, 49, 8, 8] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 353 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 940) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1) `ZINC001285964559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285964559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285964559 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)CC(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 11, 11, 11, 16, 20, 11, 11, 11, 11, 38, 42, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 20, 20, 60, 11, 38, 38, 49, 49, 49, 11, 11] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 346 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285964559 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285964559 Building ZINC001285965233 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285965233 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/941 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285965233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285965233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285965233 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 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, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 42, 42, 42, 18, 42, 18, 18, 9, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 42, 42, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 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, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/942 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285965233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285965233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285965233 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 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, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 41, 18, 41, 18, 18, 9, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 41, 41, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285965233 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 Building ZINC001285965233 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285965233 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 941) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285965233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285965233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285965233 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 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, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 42, 42, 42, 18, 42, 18, 18, 9, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 42, 42, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 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, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 942) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001285965233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285965233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001285965233 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 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, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 41, 18, 41, 18, 18, 9, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 41, 41, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 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, 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/3016/xbk-8058097.37/working/building/ZINC001285965233 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285965233 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965233 Building ZINC001285965673 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285965673 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/943 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)ccn1) `ZINC001285965673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285965673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285965673 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 12, 12, 12, 10, 10, 10, 17, 18, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 37, 37, 14, 37, 37, 37, 37, 12, 17, 17, 18, 18, 54, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 37] 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: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/944 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)ccn1) `ZINC001285965673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285965673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285965673 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 9, 9, 9, 7, 7, 7, 13, 13, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 32, 32, 18, 32, 32, 32, 32, 9, 13, 13, 13, 13, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285965673 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 Building ZINC001285965673 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285965673 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 943) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)ccn1) `ZINC001285965673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285965673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285965673 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 12, 12, 12, 10, 10, 10, 17, 18, 10, 3, 1, 6, 1, 1, 1, 1, 1, 1, 10, 37, 37, 14, 37, 37, 37, 37, 12, 17, 17, 18, 18, 54, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 37] 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: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 944) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)ccn1) `ZINC001285965673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285965673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001285965673 none Cc1cc(C(=O)NC2(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 9, 9, 9, 7, 7, 7, 13, 13, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 32, 32, 18, 32, 32, 32, 32, 9, 13, 13, 13, 13, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285965673 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285965673 Building ZINC001285968193 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285968193 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/945 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1) `ZINC001285968193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285968193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285968193 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 21, 21, 21, 36, 41, 21, 24, 24, 24, 37, 37, 37, 37, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 36, 36, 41, 41, 123, 24, 37, 37, 21, 21] 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, 41, 42, 43]) total number of confs: 292 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/946 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1) `ZINC001285968193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285968193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285968193 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 20, 20, 20, 35, 39, 20, 25, 25, 25, 40, 40, 40, 40, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 35, 35, 39, 39, 117, 25, 40, 40, 20, 20] 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, 41, 42, 43]) total number of confs: 296 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285968193 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 Building ZINC001285968193 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285968193 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 945) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1) `ZINC001285968193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285968193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285968193 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 21, 21, 21, 36, 41, 21, 24, 24, 24, 37, 37, 37, 37, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 36, 36, 41, 41, 123, 24, 37, 37, 21, 21] 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, 41, 42, 43]) total number of confs: 292 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 946) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1) `ZINC001285968193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285968193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285968193 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CCO)(NC(=O)c2nccs2)C1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 8, 1, 11, 1, 8, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 20, 20, 20, 35, 39, 20, 25, 25, 25, 40, 40, 40, 40, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 35, 35, 39, 39, 117, 25, 40, 40, 20, 20] 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, 41, 42, 43]) total number of confs: 296 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285968193 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285968193 Building ZINC001285972750 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285972750 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/947 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001285972750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285972750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285972750 none CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 35, 14, 35, 14, 14, 13, 13, 13, 23, 26, 13, 4, 1, 7, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 41, 41, 41, 41, 41, 14, 23, 23, 26, 26, 78, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 150 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, 54]) total number of confs: 304 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/948 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001285972750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285972750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285972750 none CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 35, 17, 35, 17, 17, 15, 15, 15, 28, 30, 15, 4, 1, 7, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 40, 40, 40, 40, 40, 17, 28, 28, 30, 30, 90, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 35, 35, 35] 150 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, 54]) total number of confs: 313 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285972750 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 Building ZINC001285972750 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285972750 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 947) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001285972750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285972750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285972750 none CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 35, 14, 35, 14, 14, 13, 13, 13, 23, 26, 13, 4, 1, 7, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 41, 41, 41, 41, 41, 14, 23, 23, 26, 26, 78, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35] 150 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, 54]) total number of confs: 304 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 948) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001285972750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285972750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001285972750 none CC[C@@H](C(=O)NC1(CCO)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 35, 17, 35, 17, 17, 15, 15, 15, 28, 30, 15, 4, 1, 7, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 40, 40, 40, 40, 40, 17, 28, 28, 30, 30, 90, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 35, 35, 35] 150 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, 54]) total number of confs: 313 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285972750 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285972750 Building ZINC001285976002 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285976002 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/949 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285976002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285976002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001285976002 none CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 5, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 186 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/950 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285976002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285976002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001285976002 none CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 50, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285976002 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 Building ZINC001285976002 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285976002 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 949) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001285976002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285976002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001285976002 none CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 5, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 186 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 950) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001285976002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285976002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001285976002 none CNC(=O)CC(=O)N1CC[C@H]2CC[C@@H](C1)N2C(=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', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 50, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 32, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285976002 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285976002 Building ZINC001285983346 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285983346 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/951 `/scratch/xiaobo/3016/xbk-8058097.37/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(CC1CC1)C1CCN(C(=O)C(N)=O)CC1) `ZINC001285983346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285983346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285983346 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CC1CC1)C1CCN(C(=O)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 4, 10, 10, 10, 10, 21, 21, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10, 34, 34, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/952 `/scratch/xiaobo/3016/xbk-8058097.37/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(CC1CC1)C1CCN(C(=O)C(N)=O)CC1) `ZINC001285983346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285983346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285983346 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CC1CC1)C1CCN(C(=O)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 4, 11, 11, 11, 11, 24, 24, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 37, 37, 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: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285983346 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 Building ZINC001285983346 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285983346 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 951) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(CC1CC1)C1CCN(C(=O)C(N)=O)CC1) `ZINC001285983346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285983346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285983346 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CC1CC1)C1CCN(C(=O)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 4, 10, 10, 10, 10, 21, 21, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10, 34, 34, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 952) grep: /scratch/xiaobo/3016/xbk-8058097.37/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(CC1CC1)C1CCN(C(=O)C(N)=O)CC1) `ZINC001285983346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285983346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001285983346 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CC1CC1)C1CCN(C(=O)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 4, 11, 11, 11, 11, 24, 24, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 37, 37, 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: 169 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285983346 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285983346 Building ZINC001285991816 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285991816 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/953 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285991816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991816 none CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 11, 8, 11, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 42, 42, 8, 8, 8, 8, 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, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/954 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285991816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991816 none CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 11, 9, 11, 9, 9, 9, 9, 9, 9, 3, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285991816 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 Building ZINC001285991816 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285991816 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 953) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285991816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991816 none CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 11, 8, 11, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 42, 42, 8, 8, 8, 8, 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, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 954) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285991816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991816 none CNC(=O)CC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 11, 9, 11, 9, 9, 9, 9, 9, 9, 3, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285991816 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991816 Building ZINC001285991817 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285991817 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/955 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285991817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991817 none CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 11, 7, 11, 7, 7, 7, 7, 7, 7, 3, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 39, 39, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/956 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285991817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991817 none CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 11, 7, 11, 7, 7, 7, 7, 7, 7, 3, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 42, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285991817 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 Building ZINC001285991817 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001285991817 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 955) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001285991817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991817 none CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 11, 7, 11, 7, 7, 7, 7, 7, 7, 3, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 39, 39, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 956) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001285991817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001285991817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001285991817 none CNC(=O)CC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 11, 7, 11, 7, 7, 7, 7, 7, 7, 3, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 42, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001285991817 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001285991817 Building ZINC001286002468 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002468 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/957 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001286002468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001286002468 none CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 20, 19, 20, 19, 13, 9, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50, 50, 31, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/958 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001286002468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001286002468 none CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 21, 19, 21, 19, 13, 11, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50, 50, 31, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002468 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 Building ZINC001286002468 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002468 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 957) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001286002468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001286002468 none CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 20, 19, 20, 19, 13, 9, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50, 50, 31, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 958) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001286002468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001286002468 none CCOc1cnc(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 21, 19, 21, 19, 13, 11, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 19, 31, 31, 50, 50, 50, 50, 50, 31, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002468 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002468 Building ZINC001286002566 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002566 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/959 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001286002566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001286002566 none CC(C)[C@H](C(=O)N1CC(N(C)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', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 13, 38, 13, 13, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/960 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001286002566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001286002566 none CC(C)[C@H](C(=O)N1CC(N(C)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', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 37, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002566 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 Building ZINC001286002566 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002566 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 959) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001286002566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001286002566 none CC(C)[C@H](C(=O)N1CC(N(C)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', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 13, 38, 13, 13, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 960) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CC(C)[C@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001286002566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001286002566 none CC(C)[C@H](C(=O)N1CC(N(C)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', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 37, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002566 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002566 Building ZINC001286002596 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002596 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/961 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/961' -> `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)C1CN(C(=O)CCCCNC(N)=O)C1) `ZINC001286002596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002596 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 14, 19, 21, 38, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 21, 21, 21, 21, 38, 38, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/962 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/962' -> `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)C1CN(C(=O)CCCCNC(N)=O)C1) `ZINC001286002596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002596 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 8, 8, 20, 24, 24, 44, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 24, 24, 24, 24, 44, 44, 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, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002596 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 Building ZINC001286002596 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002596 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 961) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1) `ZINC001286002596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002596 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 14, 19, 21, 38, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 21, 21, 21, 21, 38, 38, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 962) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1) `ZINC001286002596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002596 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 8, 8, 20, 24, 24, 44, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 24, 24, 24, 24, 44, 44, 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, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002596 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002596 Building ZINC001286002603 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002603 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/963 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/963' -> `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)C1CN(C(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001286002603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002603 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 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, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 24, 24, 28, 28, 28, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 28, 28, 28, 28, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/964 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/964' -> `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)C1CN(C(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001286002603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002603 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 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, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 27, 27, 32, 32, 32, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 32, 32, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002603 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 Building ZINC001286002603 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002603 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 963) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001286002603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002603 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 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, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 24, 24, 28, 28, 28, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 28, 28, 28, 28, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 964) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001286002603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002603 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)C(C)(C)S(C)(=O)=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 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, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 27, 27, 32, 32, 32, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 32, 32, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002603 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002603 Building ZINC001286002771 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002771 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/965 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001286002771 none Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 23, 33, 23, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/966 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001286002771 none Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 34, 24, 19, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002771 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 Building ZINC001286002771 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002771 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 965) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001286002771 none Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 23, 33, 23, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 966) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001286002771 none Cc1nn(C)c(F)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 24, 34, 24, 19, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 24, 24, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002771 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002771 Building ZINC001286002804 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002804 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/967 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/967' -> `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)C1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001286002804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002804 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 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]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/968 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/968' -> `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)C1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001286002804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002804 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 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]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002804 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 Building ZINC001286002804 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002804 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 967) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001286002804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002804 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 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]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 968) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)C1) `ZINC001286002804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286002804 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2nc[nH]c3nccc2-3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 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]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002804 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002804 Building ZINC001286002907 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002907 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/969 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286002907 none COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 50, 30, 22, 30, 22, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/970 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286002907 none COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 50, 50, 29, 21, 29, 21, 16, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002907 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 Building ZINC001286002907 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286002907 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 969) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286002907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286002907 none COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 50, 30, 22, 30, 22, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 970) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286002907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286002907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286002907 none COc1nc(C)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 50, 50, 29, 21, 29, 21, 16, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286002907 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286002907 Building ZINC001286003495 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003495 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/971 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003495 none C[C@@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [35, 18, 35, 12, 18, 12, 12, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 12, 12, 12, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/972 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003495 none C[C@@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [37, 18, 37, 14, 18, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 37, 37, 37, 14, 14, 14, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003495 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 Building ZINC001286003495 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003495 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 971) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003495 none C[C@@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [35, 18, 35, 12, 18, 12, 12, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 12, 12, 12, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 972) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003495 none C[C@@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [37, 18, 37, 14, 18, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 37, 37, 37, 14, 14, 14, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003495 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003495 Building ZINC001286003497 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003497 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/973 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003497 none C[C@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [37, 19, 37, 11, 19, 11, 11, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 11, 37, 50, 50, 50, 50, 50, 37, 37, 37, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/974 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003497 none C[C@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [35, 20, 35, 12, 20, 12, 12, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 12, 12, 12, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003497 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 Building ZINC001286003497 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003497 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 973) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003497 none C[C@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [37, 19, 37, 11, 19, 11, 11, 5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 11, 37, 50, 50, 50, 50, 50, 37, 37, 37, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 974) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001286003497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001286003497 none C[C@H](C(=O)N1CC(N(C)C(=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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [35, 20, 35, 12, 20, 12, 12, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 12, 12, 12, 5, 5, 5, 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, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003497 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003497 Building ZINC001286003506 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003506 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/975 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003506 none COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 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] 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, 30, 19, 30, 19, 17, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 100, 19, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/976 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003506 none COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 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] 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, 31, 22, 31, 22, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 100, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003506 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 Building ZINC001286003506 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003506 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 975) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003506 none COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 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] 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, 30, 19, 30, 19, 17, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 100, 19, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 976) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003506 none COc1ccnc(O)c1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 4, 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] 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, 31, 22, 31, 22, 17, 9, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 100, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003506 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003506 Building ZINC001286003526 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003526 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/977 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003526 none COc1cc(O)ncc1C(=O)N1CC(N(C)C(=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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 3, 7, 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] 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, 31, 24, 31, 24, 18, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 100, 50, 24, 24, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/978 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003526 none COc1cc(O)ncc1C(=O)N1CC(N(C)C(=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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 3, 7, 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] 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, 28, 21, 28, 21, 16, 8, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 100, 50, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003526 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 Building ZINC001286003526 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003526 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 977) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1cc(O)ncc1C(=O)N1CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003526 none COc1cc(O)ncc1C(=O)N1CC(N(C)C(=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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 3, 7, 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] 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, 31, 24, 31, 24, 18, 7, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 100, 50, 24, 24, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 978) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: COc1cc(O)ncc1C(=O)N1CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001286003526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001286003526 none COc1cc(O)ncc1C(=O)N1CC(N(C)C(=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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 3, 7, 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] 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, 28, 21, 28, 21, 16, 8, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 100, 50, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003526 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003526 Building ZINC001286003560 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003560 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/979 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/979' -> `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)C1CN(C(=O)c2csc(O)n2)C1) `ZINC001286003560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003560 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 34, 34, 50, 50, 50, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 50, 150, 23, 23] 150 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 301 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/980 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/980' -> `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)C1CN(C(=O)c2csc(O)n2)C1) `ZINC001286003560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003560 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 40, 40, 50, 50, 50, 50, 50, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 150, 28, 28] 150 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 319 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003560 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 Building ZINC001286003560 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003560 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 979) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)n2)C1) `ZINC001286003560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003560 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 34, 34, 50, 50, 50, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 50, 150, 23, 23] 150 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 301 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 980) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)n2)C1) `ZINC001286003560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003560 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2csc(O)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 40, 40, 50, 50, 50, 50, 50, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 150, 28, 28] 150 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 319 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003560 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003560 Building ZINC001286003616 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003616 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/981 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/981' -> `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)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003616 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/982 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/982' -> `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)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003616 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003616 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 Building ZINC001286003616 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003616 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 981) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003616 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 982) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003616 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003616 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003616 Building ZINC001286003620 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003620 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/983 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/983' -> `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)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003620 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/984 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/984' -> `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)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003620 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003620 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 Building ZINC001286003620 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003620 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 983) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003620 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 984) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C1) `ZINC001286003620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003620 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003620 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003620 Building ZINC001286003729 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003729 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/985 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/985' -> `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)C1CN(C(=O)CC2OCCCO2)C1) `ZINC001286003729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003729 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 10, 39, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 39, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/986 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/986' -> `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)C1CN(C(=O)CC2OCCCO2)C1) `ZINC001286003729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003729 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 10, 38, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 38, 38, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003729 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 Building ZINC001286003729 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003729 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 985) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)C1) `ZINC001286003729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003729 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 10, 39, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 39, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 986) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)C1) `ZINC001286003729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003729 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)CC2OCCCO2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 10, 38, 50, 50, 50, 50, 50, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 38, 38, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003729 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003729 Building ZINC001286003892 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003892 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/987 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/987' -> `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)C1CN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001286003892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003892 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/988 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/988' -> `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)C1CN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001286003892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003892 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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, 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, 7] 0 hydrogens need 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, 16, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 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]) total number of confs: 134 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003892 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 Building ZINC001286003892 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286003892 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 987) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001286003892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286003892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003892 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 988) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001286003892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286003892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286003892 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]cnc3c2)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', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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, 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, 7] 0 hydrogens need 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, 16, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 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]) total number of confs: 134 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286003892 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286003892 Building ZINC001286004078 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004078 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/989 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/989' -> `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)C1CN(C(=O)Cn2ccccc2=O)C1) `ZINC001286004078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004078 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 11, 11, 39, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 39, 50, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/990 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/990' -> `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)C1CN(C(=O)Cn2ccccc2=O)C1) `ZINC001286004078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004078 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 11, 11, 41, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 41, 50, 50, 50, 50, 7, 7] 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004078 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 Building ZINC001286004078 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004078 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 989) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=O)C1) `ZINC001286004078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004078 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 11, 11, 39, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 39, 50, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 990) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=O)C1) `ZINC001286004078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004078 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)Cn2ccccc2=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 11, 11, 41, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 41, 50, 50, 50, 50, 7, 7] 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004078 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004078 Building ZINC001286004152 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004152 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/991 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/991' -> `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)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004152 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/992 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/992' -> `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)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004152 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004152 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 Building ZINC001286004152 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004152 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 991) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004152 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 992) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004152 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 14, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004152 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004152 Building ZINC001286004153 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004153 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/993 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/993' -> `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)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004153 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/994 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/994' -> `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)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004153 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 18, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004153 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 Building ZINC001286004153 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004153 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 993) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004153 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 994) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)C1) `ZINC001286004153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004153 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CCc3c[nH]nc3C2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 6, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 18, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 38, 37, 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, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004153 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004153 Building ZINC001286004165 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004165 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/995 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/995' -> `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)C1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001286004165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004165 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 13, 13] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/996 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/996' -> `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)C1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001286004165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004165 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 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]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004165 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 Building ZINC001286004165 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004165 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 995) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001286004165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004165 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 13, 13] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 996) grep: /scratch/xiaobo/3016/xbk-8058097.37/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)C1) `ZINC001286004165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004165 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cnc3[nH]nnc3c2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 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: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 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]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004165 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004165 Building ZINC001286004340 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004340 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/997 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/997' -> `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)C1CN(C(=O)c2cn(C)nc2Cl)C1) `ZINC001286004340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004340 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 16, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 26, 26, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/998 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/998' -> `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)C1CN(C(=O)c2cn(C)nc2Cl)C1) `ZINC001286004340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004340 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 16, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004340 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 Building ZINC001286004340 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004340 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 997) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)C1) `ZINC001286004340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004340 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 16, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 26, 26, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 998) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)C1) `ZINC001286004340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001286004340 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)c2cn(C)nc2Cl)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 16, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 33, 33, 50, 50, 50, 50, 50, 50, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004340 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004340 Building ZINC001286004400 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004400 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/999 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001286004400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001286004400 none CCc1c(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 20, 12, 20, 12, 10, 7, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 32] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/3016/xbk-8058097.37/working/3D/1000 `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001286004400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001286004400 none CCc1c(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 24, 15, 24, 15, 11, 6, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 50, 50, 50, 50, 50, 15, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 35] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004400 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 Building ZINC001286004400 mkdir: created directory `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001286004400 mkdir: created directory `0' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 0 (index: 999) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1c(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001286004400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001286004400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001286004400 none CCc1c(C(=O)N2CC(N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 20, 12, 20, 12, 10, 7, 4, 5, 1, 4, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 32] 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 mkdir: created directory `1' /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1 /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Protomer 1 (index: 1000) grep: /scratch/xiaobo/3016/xbk-8058097.37/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: CCc1c(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001286004400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001286004400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001286004400 none CCc1c(C(=O)N2CC(N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 24, 15, 24, 15, 11, 6, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 50, 50, 50, 50, 50, 15, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 35] 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Finished preparing ZINC001286004400 Recording results /scratch/xiaobo/3016/xbk-8058097.37/working /scratch/xiaobo/3016/xbk-8058097.37 Appending to /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.* 1: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/1.* 0: /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400/0.* Removing working files in /scratch/xiaobo/3016/xbk-8058097.37/working/building/ZINC001286004400 /scratch/xiaobo/3016/xbk-8058097.37 Compressing combined databse files /scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/3016/xbk-8058097.37/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/3016/xbk-8058097.37/working/3D/1001' removed directory: `/scratch/xiaobo/3016/xbk-8058097.37/working/3D' rmdir: removing directory, `/scratch/xiaobo/3016/xbk-8058097.37/working/building' rmdir: removing directory, `/scratch/xiaobo/3016/xbk-8058097.37/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/3016/xbk-8058097.37' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbk' `/scratch/xiaobo/3016/xbk-8058097.37/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbk/finished' `/scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbk/finished/xbk.db2.gz' removed `/scratch/xiaobo/3016/xbk-8058097.37/finished/xbk.db2.gz' removed directory: `/scratch/xiaobo/3016/xbk-8058097.37/finished' removed directory: `/scratch/xiaobo/3016/xbk-8058097.37'